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Crystal Structure of human phosphoglycerate kinase bound to D-CDP
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 38.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.579 α = 78.92 b = 55.588 β = 84.32 c = 93.805 γ = 82.95
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 2007-03-26 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 1.8 50.96 87.2 0.042 14.6 1.9 54699 54699 21.6
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) 1.8 1.9 50.2 0.37 3 1.8 3838
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 1.8 50.94 54697 54697 1703 87.21 0.17137 0.17137 0.16925 0.171 0.2411 RANDOM 23.435
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] -0.01 0.01 -0.03 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.316 r_dihedral_angle_4_deg 17.481 r_dihedral_angle_3_deg 15.865 r_scangle_it 8.451 r_dihedral_angle_1_deg 6.886 r_scbond_it 5.595 r_mcangle_it 2.803 r_angle_refined_deg 2 r_mcbond_it 1.753 r_chiral_restr 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.316 r_dihedral_angle_4_deg 17.481 r_dihedral_angle_3_deg 15.865 r_scangle_it 8.451 r_dihedral_angle_1_deg 6.886 r_scbond_it 5.595 r_mcangle_it 2.803 r_angle_refined_deg 2 r_mcbond_it 1.753 r_chiral_restr 0.152 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6004 Nucleic Acid Atoms Solvent Atoms 738 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing