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Crystal structure of GRP78 (70kDa heat shock protein 5 / BiP) ATPase domain in complex with ADP and calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 26% PEG6000, 0.2M CaCl2, 0.1MNaOAc Ph5
Crystal Properties Matthews coefficient Solvent content 2.37 48.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.359 α = 78.07 b = 51.862 β = 86.72 c = 93.082 γ = 62.28
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.88 29.14 97.4 0.063 0.999 18.2 8.9 62200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.92 0.989 0.669
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 3IUC 1.88 29.13 59027 3141 97.56 0.2097 0.2088 0.2167 0.2249 0.2306 RANDOM 32.466
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 0.04 1.21 -0.49 -0.54 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.267 r_dihedral_angle_3_deg 11.591 r_dihedral_angle_4_deg 9.599 r_dihedral_angle_1_deg 5.397 r_angle_refined_deg 1.163 r_angle_other_deg 1.101 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.267 r_dihedral_angle_3_deg 11.591 r_dihedral_angle_4_deg 9.599 r_dihedral_angle_1_deg 5.397 r_angle_refined_deg 1.163 r_angle_other_deg 1.101 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5802 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing