Experiment | |
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Method _exptl.method | X-RAY DIFFRACTION The method used in the experiment. |
Experimental protocol _diffrn_radiation.pdbx_diffrn_protocol | SINGLE WAVELENGTH SINGLE WAVELENGTH, LAUE, or MAD. |
Source type _diffrn_source.source | ROTATING ANODE The general class of the radiation source. |
Source details _diffrn_source.type | RIGAKU MICROMAX-007 HF The make, model or name of the source of radiation. |
Temperature [K] _diffrn.ambient_temp | 100 The mean temperature in kelvins at which the intensities were |
Detector technology _diffrn_detector.detector | IMAGE PLATE The general class of the radiation detector. |
Collection date _diffrn_detector.pdbx_collection_date | 2012-12-20 The date of data collection. |
Detector _diffrn_detector.type | MAR scanner 345 mm plate The make, model or name of the detector device used. |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 1.5418 Comma separated list of wavelengths or wavelength range. |
Software | |
Data scaling #1 _software.classification | SCALA (3.3.20) The classification of the program according to its |
Data scaling #2 _software.classification | XDS The classification of the program according to its |
Refinement _software.classification | BUSTER (2.10.0) The classification of the program according to its |
General information | |
Spacegroup name _symmetry.space_group_name_H-M | P 21 21 21 Hermann-Mauguin space-group symbol. Note that the |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 47.707 Unit-cell length a corresponding to the structure reported in 52.877 Unit-cell length b corresponding to the structure reported in 90.873 Unit-cell length c corresponding to the structure reported in 90.0 Unit-cell angle alpha of the reported structure in degrees. 90.0 Unit-cell angle beta of the reported structure in degrees. 90.0 Unit-cell angle gamma of the reported structure in degrees. |
Wavelength _diffrn_radiation_wavelength.wavelength | 1.54180 ÅThe radiation wavelength in angstroms. |
Data quality metrics | Overall | InnerShell | OuterShell |
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Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 45.703 The largest value in angstroms for the interplanar spacings | 35.421 The highest value in angstroms for the interplanar spacings | 2.590 The highest value in angstroms for the interplanar spacings |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 2.457 The smallest value in angstroms for the interplanar spacings | 7.770 The smallest value in angstroms for the interplanar spacings | 2.457 The smallest value in angstroms for the interplanar spacings |
Rmerge _reflns.pdbx_Rsym_value _reflns_shell.Rmerge_I_obs | 0.109 The R sym value as a decimal number. | 0.028 The value of Rmerge(I) for reflections classified as 'observed' | 0.378 The value of Rmerge(I) for reflections classified as 'observed' |
Rmeas _reflns.pdbx_Rrim_I_all | 0.129 The redundancy-independent merging R factor value Rrim, | - | - |
Rpim _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all | 0.067 The precision-indicating merging R factor value Rpim, | 0.021 The precision-indicating merging R factor value Rpim, | 0.232 The precision-indicating merging R factor value Rpim, |
Total number of observations _reflns.pdbx_number_measured_all _reflns_shell.number_measured_all | 30830 Total number of measured reflections. | 998 The total number of reflections measured for this | 4165 The total number of reflections measured for this |
Total number unique _reflns.number_obs _reflns_shell.number_unique_all | 8737 The number of reflections in the REFLN list (not the DIFFRN_REFLN | 323 The total number of measured reflections which are symmetry- | 1194 The total number of measured reflections which are symmetry- |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs | 10.20 The mean of the ratio of the intensities to their | 7.00 The ratio of the mean of the intensities of the reflections | 2.00 The ratio of the mean of the intensities of the reflections |
Completeness [%] _reflns.percent_possible_obs _reflns_shell.percent_possible_all | 98.9 The percentage of geometrically possible reflections represented | 98.5 The percentage of geometrically possible reflections represented | 96.3 The percentage of geometrically possible reflections represented |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 3.5 Overall redundancy for this data set. | 3.1 Redundancy for the current shell. | 3.5 Redundancy for the current shell. |
CC(1/2) | - | - | - |
Refinement | |
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PDB entry ID _entry.id | 4PH1 |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2014-05-03 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 35.4 - 2.460 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.1993 / 0.2533 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | a number of search probes were generated by comparative modelling with the Rosetta suite [Das, R. & Baker, D. Macromolecular modeling with rosetta (2008) Annu Rev Biochem 77, 363-82], using PDB ID 3h47 as a template. In this way, 10000 models were obtained, scored and clustered. Several top ranking models gave solutions in MR using the program Phaser. To note, using PDB 3H47 (or any other available PDB with similar sequence) did not produce right solutions. |