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Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 291 2.6M NaKPO4, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.616 α = 79.18 b = 55.79 β = 84.33 c = 93.23 γ = 83.23
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 ADSC QUANTUM 315 2007-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.933 ESRF ID29
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 1.85 91.29 77.1 0.048 14 1.9 44499 44499 21.22
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) 1.85 1.95 50.4 0.34 1.9 1.8 3309
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VJC 1.85 50.1 44499 44499 1435 77.08 0.19383 0.19383 0.19126 0.1937 0.27281 RANDOM 21.353
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] -0.88 0.01 -0.35 -1.27 0.91 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.373 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_1_deg 6.886 r_scangle_it 4.605 r_scbond_it 2.991 r_angle_refined_deg 1.905 r_mcangle_it 1.831 r_mcbond_it 1.09 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.373 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_1_deg 6.886 r_scangle_it 4.605 r_scbond_it 2.991 r_angle_refined_deg 1.905 r_mcangle_it 1.831 r_mcbond_it 1.09 r_chiral_restr 0.136 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5949 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing