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The structure of human GPX8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P31 PDB entry 2p31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 2 M ammonium sulfate, 1.5 % PEG 400, 0.1 M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.75 55.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.688 α = 90 b = 120.854 β = 119.38 c = 75.603 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 225 mm CCD 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 44.99 99.7 0.092 8.9 4.1 47649 47649 29
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 2.11 99.2 0.394 3.1 4.1 6901
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2p31 2 44.99 45240 45240 2404 99.57 0.17217 0.17217 0.17073 0.1762 0.1989 0.2045 RANDOM 26.557
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] 0.22 0.03 0.66 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.389 r_dihedral_angle_4_deg 14.314 r_dihedral_angle_3_deg 13.106 r_dihedral_angle_1_deg 6.024 r_scangle_it 5.637 r_scbond_it 4.361 r_mcangle_it 2.636 r_mcbond_it 1.985 r_angle_refined_deg 1.217 r_angle_other_deg 0.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.389 r_dihedral_angle_4_deg 14.314 r_dihedral_angle_3_deg 13.106 r_dihedral_angle_1_deg 6.024 r_scangle_it 5.637 r_scbond_it 4.361 r_mcangle_it 2.636 r_mcbond_it 1.985 r_angle_refined_deg 1.217 r_angle_other_deg 0.892 r_mcbond_other 0.444 r_symmetry_vdw_other 0.236 r_nbd_refined 0.195 r_nbd_other 0.183 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.166 r_symmetry_vdw_refined 0.139 r_symmetry_hbond_refined 0.094 r_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4203 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing