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Crystal Structure of human phosphoglycerate kinase bound to D-ADP
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 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.956 α = 90 b = 106.627 β = 97.3 c = 50.35 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 AREA DETECTOR 2007-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.934 ESRF ID14-4
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 45.22 0.69 0.048 11.3 2.6 16987 16987 19.2
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) 2 2.11 0.31 0.323 2.9 2 1136
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VJC 2 45.22 16987 466 68.74 0.17782 0.17557 0.25828 RANDOM 19.739
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] 0.12 0.61 -0.58 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.472 r_dihedral_angle_4_deg 19.349 r_dihedral_angle_3_deg 17.235 r_dihedral_angle_1_deg 6.619 r_scangle_it 4.43 r_scbond_it 2.696 r_angle_refined_deg 1.697 r_mcangle_it 1.542 r_mcbond_it 0.863 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.472 r_dihedral_angle_4_deg 19.349 r_dihedral_angle_3_deg 17.235 r_dihedral_angle_1_deg 6.619 r_scangle_it 4.43 r_scbond_it 2.696 r_angle_refined_deg 1.697 r_mcangle_it 1.542 r_mcbond_it 0.863 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3024 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing