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Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ADP and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EXW
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 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.55 α = 90 b = 74.802 β = 98.6 c = 89.22 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 1.82 50 99.9 0.077 13.4 5 64199
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 1.82 1.85 99.9 0.457 4.6 3191
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 5EXW 1.85 44.31 58565 3120 99.83 0.1674 0.1654 0.1738 0.2053 0.2107 RANDOM 32.051
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] 1.21 -1.12 -0.45 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_3_deg 11.873 r_dihedral_angle_1_deg 5.227 r_mcangle_it 1.656 r_angle_refined_deg 1.34 r_mcbond_it 1.157 r_mcbond_other 1.152 r_angle_other_deg 0.727 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_3_deg 11.873 r_dihedral_angle_1_deg 5.227 r_mcangle_it 1.656 r_angle_refined_deg 1.34 r_mcbond_it 1.157 r_mcbond_other 1.152 r_angle_other_deg 0.727 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 534 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction MOLREP phasing