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X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O8A PDB ENTRY 2O8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 7-12% PEG3350, 0.1 M BICINE, PH 9.0 SOAKING IN RESERVOIR ENRICHED WITH 50MM H2O2 FOR 10 MINS CRYOPROTECTION IN RESEVOIR ENRICHED WITH 25% MPD
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.45 α = 90 b = 105.22 β = 90.34 c = 89.82 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 45.4 97.5 0.08 7.9 3.3 35328 -1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 97.3 0.62 2.1 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2O8A 2.19 45.4 33509 1742 95.69 0.17518 0.17336 0.1759 0.21146 0.2132 RANDOM 47.211
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -32.79 -4.58 46 -13.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.751 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 5.955 r_mcangle_it 4.351 r_scbond_it 3.882 r_mcbond_it 2.918 r_mcbond_other 2.917 r_angle_refined_deg 1.267 r_angle_other_deg 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.751 r_dihedral_angle_4_deg 16.118 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 5.955 r_mcangle_it 4.351 r_scbond_it 3.882 r_mcbond_it 2.918 r_mcbond_other 2.917 r_angle_refined_deg 1.267 r_angle_other_deg 0.81 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4745 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing