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Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 2'-deoxy-ADP and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EY4 PDB entry 5EY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 24-26% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.01 38.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.347 α = 90 b = 74.448 β = 97.67 c = 85.882 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 CCD RAYONIX MX-300 2015-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.59 50 99.6 0.078 17.2 4.7 94555
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 1.59 1.62 96.9 0.491 4.4 4581
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5EY4 1.6 37.95 87787 4664 99.66 0.1756 0.1741 0.2037 0.2175 RANDOM 22.056
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] 0.91 -0.76 -0.66 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.952 r_dihedral_angle_4_deg 13.09 r_dihedral_angle_3_deg 10.784 r_dihedral_angle_1_deg 5.059 r_mcangle_it 1.823 r_mcbond_it 1.272 r_mcbond_other 1.269 r_angle_refined_deg 1.249 r_angle_other_deg 0.704 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.952 r_dihedral_angle_4_deg 13.09 r_dihedral_angle_3_deg 10.784 r_dihedral_angle_1_deg 5.059 r_mcangle_it 1.823 r_mcbond_it 1.272 r_mcbond_other 1.269 r_angle_refined_deg 1.249 r_angle_other_deg 0.704 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5920 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 98
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing