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The R62Q clinical variant of human bisphosphoglycerate mutase (hBPGM).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.09 M NPS (0.3M Sodium Nitrate, 0.3 Sodium Phosphate dibasic, 0.3M Ammonium Sulfate), 0.1 M of Buffer System2 (Sodium HEPES; MOPS (acid)) pH 7.5, 30 % v/v of Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.55 α = 86.86 b = 47.242 β = 84.12 c = 143.043 γ = 83.17
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 EIGER X 4M 2023-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 71.08 93.9 0.194 0.247 0.151 0.951 3.2 2.7 31472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 94.5 0.757 0.966 0.591 0.513 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 71.08 1.96 31272 1553 93.28 0.2107 0.2079 0.2066 0.2636 0.2647
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.278 f_angle_d 0.542 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8009 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement Aimless data scaling xia2 data reduction MOLREP phasing PDB_EXTRACT data extraction