☰ Navigation Tabs
The complete reaction cycle of human phosphoglycerate kinase: The open binary complex with 3PG
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 8 30% PEG4000, 100MM TRIS PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.57 α = 90 b = 73.01 β = 90 c = 93.64 γ = 90
Symmetry Space Group P 21 21 2
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 221 2009-06-26 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 1.74 20 98.9 0.1 8.1 4.1 43561 3 22.6
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 1.74 1.83 100 0.29 3.2 3.7
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 1.74 20 41325 2178 98.55 0.20807 0.20571 0.219 0.2525 0.2603 RANDOM 22.249
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] -0.26 0.59 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.792 r_dihedral_angle_4_deg 22.637 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_1_deg 6.367 r_scangle_it 4.849 r_scbond_it 3.144 r_angle_refined_deg 1.856 r_mcangle_it 1.733 r_mcbond_it 1.097 r_angle_other_deg 1.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.792 r_dihedral_angle_4_deg 22.637 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_1_deg 6.367 r_scangle_it 4.849 r_scbond_it 3.144 r_angle_refined_deg 1.856 r_mcangle_it 1.733 r_mcbond_it 1.097 r_angle_other_deg 1.037 r_mcbond_other 0.39 r_chiral_restr 0.13 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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 3096 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing