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The active form of phosphoglycerate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Resolve PDB output based on MAD phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 291 1.18 M to 1.25 M AmSO4, 100 mM KPO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.62 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.159 α = 90 b = 76.159 β = 90 c = 354.144 γ = 90
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 SBC 2002-12-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9537,0.9795,0.9797 APS 19-ID
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 2.24 50 96.3 0.089 20.2 12.2 92508 92508
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.28 77.3 0.45 2.3 2.1 3598
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 MAD THROUGHOUT Resolve PDB output based on MAD phasing 2.24 50 96093 85989 4538 94.21 0.18891 0.18891 0.18648 0.2039 0.23512 0.2445 RANDOM 38.322
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] 0.79 0.79 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_4_deg 18.094 r_dihedral_angle_3_deg 17.537 r_dihedral_angle_1_deg 6.534 r_scangle_it 3.013 r_scbond_it 1.892 r_angle_refined_deg 1.692 r_mcangle_it 1.004 r_angle_other_deg 0.836 r_mcbond_it 0.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_4_deg 18.094 r_dihedral_angle_3_deg 17.537 r_dihedral_angle_1_deg 6.534 r_scangle_it 3.013 r_scbond_it 1.892 r_angle_refined_deg 1.692 r_mcangle_it 1.004 r_angle_other_deg 0.836 r_mcbond_it 0.767 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.215 r_symmetry_vdw_other 0.21 r_xyhbond_nbd_refined 0.208 r_nbd_other 0.187 r_symmetry_vdw_refined 0.185 r_nbtor_refined 0.179 r_mcbond_other 0.128 r_nbtor_other 0.09 r_chiral_restr 0.081 r_xyhbond_nbd_other 0.053 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12308 Nucleic Acid Atoms Solvent Atoms 1346 Heterogen Atoms 311
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing