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Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 7-deaza-ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LDN PDB entry 3LDN
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 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.682 α = 90 b = 74.826 β = 98.84 c = 89.658 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 2015-05-06 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 Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.851 88.593 100 0.055 0.062 0.027 19.1 4.9 57406 57406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.176 0.176 0.085 3.6 5 8337
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 3LDN 1.9 40 54459 2910 99.82 0.1673 0.1651 0.1744 0.2083 0.2132 RANDOM 27.278
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] 0.6 -0.93 -0.19 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.249 r_dihedral_angle_3_deg 11.937 r_dihedral_angle_4_deg 11.32 r_dihedral_angle_1_deg 5.178 r_mcangle_it 1.728 r_angle_refined_deg 1.177 r_mcbond_it 1.169 r_mcbond_other 1.166 r_angle_other_deg 0.713 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.249 r_dihedral_angle_3_deg 11.937 r_dihedral_angle_4_deg 11.32 r_dihedral_angle_1_deg 5.178 r_mcangle_it 1.728 r_angle_refined_deg 1.177 r_mcbond_it 1.169 r_mcbond_other 1.166 r_angle_other_deg 0.713 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5905 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing