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The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP, 3PG and aluminium tetrafluoride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C39 PDB ENTRY 3C39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 22% PEG2000MME, 0.1M BIS/TRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.19 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.22 α = 90 b = 91.92 β = 90 c = 108.14 γ = 90
Symmetry Space Group P 21 21 21
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 CCD GE211 2009-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.5 20 97.4 0.06 11.4 2.8 61523 3 14.8
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 1.5 1.58 96.2 0.3 3 2.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3C39 1.5 20 58365 3120 96.81 0.16584 0.16415 0.2009 0.19763 0.2297 RANDOM 6.404
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] 0.89 -0.31 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.046 r_dihedral_angle_4_deg 16.505 r_dihedral_angle_3_deg 12.775 r_dihedral_angle_1_deg 9.842 r_scangle_it 3.285 r_scbond_it 2.043 r_angle_refined_deg 1.566 r_mcangle_it 1.136 r_angle_other_deg 0.906 r_mcbond_it 0.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.046 r_dihedral_angle_4_deg 16.505 r_dihedral_angle_3_deg 12.775 r_dihedral_angle_1_deg 9.842 r_scangle_it 3.285 r_scbond_it 2.043 r_angle_refined_deg 1.566 r_mcangle_it 1.136 r_angle_other_deg 0.906 r_mcbond_it 0.667 r_mcbond_other 0.212 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3040 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing