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X-ray structure of the human PP1 gamma catalytic subunit treated with ascorbate
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 19.3 % PEG 3350, 200 MM NACL, 100 MM TRIS PH 9.0 SOAKING IN RESERVOIR ENRICHED BY 25MM ASCORBATE FOR 30 MINUTES CRYOPROTECTION 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.55 α = 90 b = 90.24 β = 90.05 c = 91.13 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 2M 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.96 64.12 94.7 0.08 11.7 4 42357 -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 1.96 2.01 95.6 0.61 2.5 4
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 1.96 64.12 40219 2111 94.25 0.16836 0.16667 0.1704 0.20065 0.1989 RANDOM 31.321
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] -16.21 2.22 33.48 -17.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.047 r_dihedral_angle_4_deg 12.957 r_dihedral_angle_3_deg 12.835 r_dihedral_angle_1_deg 5.472 r_mcangle_it 1.844 r_scbond_it 1.116 r_mcbond_it 1.097 r_mcbond_other 1.094 r_angle_refined_deg 0.998 r_angle_other_deg 0.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.047 r_dihedral_angle_4_deg 12.957 r_dihedral_angle_3_deg 12.835 r_dihedral_angle_1_deg 5.472 r_mcangle_it 1.844 r_scbond_it 1.116 r_mcbond_it 1.097 r_mcbond_other 1.094 r_angle_refined_deg 0.998 r_angle_other_deg 0.757 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4748 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing