☰ Navigation Tabs
The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP and 1,3- bisphosphoglycerate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WZB PDB ENTRY 2WZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M BIS/TRIS PH 6.5, 21% P2000MME
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.73 α = 90 b = 91.75 β = 90 c = 108.31 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 GE 211 2009-05-06 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 2.1 20 99.1 0.08 10.2 2.8 22995 3 25.2
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 2.1 2.21 99.8 0.32 3 2.8
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 2WZB 2.1 20 21765 1184 98.59 0.19488 0.19249 0.2029 0.23795 0.2424 RANDOM 10.736
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] -0.15 1.73 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.431 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 14.065 r_dihedral_angle_1_deg 6.453 r_scangle_it 2.553 r_scbond_it 1.599 r_angle_refined_deg 1.401 r_mcangle_it 0.873 r_angle_other_deg 0.845 r_mcbond_it 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.431 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 14.065 r_dihedral_angle_1_deg 6.453 r_scangle_it 2.553 r_scbond_it 1.599 r_angle_refined_deg 1.401 r_mcangle_it 0.873 r_angle_other_deg 0.845 r_mcbond_it 0.48 r_mcbond_other 0.126 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 3063 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing