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Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EXW PDB entry 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 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.965 α = 90 b = 74.823 β = 98.85 c = 90.222 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 MARMOSAIC 300 mm CCD 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 1.9 44.47 99.9 0.112 0.131 0.067 8.3 3.8 58009 58009
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 0.654 0.654 0.39 1.1 3.8 8461
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 5EXW 1.9 44.47 55006 2942 99.71 0.1832 0.1809 0.1889 0.2279 0.2336 RANDOM 31.738
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] 0.67 -1.16 -0.06 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.098 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_4_deg 10.448 r_dihedral_angle_1_deg 5.212 r_mcangle_it 1.939 r_mcbond_it 1.314 r_mcbond_other 1.313 r_angle_refined_deg 1.273 r_angle_other_deg 0.746 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.098 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_4_deg 10.448 r_dihedral_angle_1_deg 5.212 r_mcangle_it 1.939 r_mcbond_it 1.314 r_mcbond_other 1.313 r_angle_refined_deg 1.273 r_angle_other_deg 0.746 r_chiral_restr 0.076 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 5905 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing