☰ Navigation Tabs
Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 2'-deoxy-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 2.02 39.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.456 α = 90 b = 74.781 β = 98.25 c = 85.747 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 ADSC QUANTUM 315r 2015-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.86 34.22 99.7 0.059 0.066 0.03 19.2 4.5 59159
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.89 98.5 0.216 0.251 0.126 0.949 3.7 2911
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 1.86 34 56062 2980 99.34 0.1746 0.1726 0.1806 0.2115 0.2184 RANDOM 26.782
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] 0.58 -0.69 -0.44 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.341 r_dihedral_angle_4_deg 14.619 r_dihedral_angle_3_deg 12.15 r_dihedral_angle_1_deg 5.165 r_mcangle_it 1.37 r_angle_refined_deg 1.226 r_mcbond_it 0.884 r_mcbond_other 0.882 r_angle_other_deg 0.714 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.341 r_dihedral_angle_4_deg 14.619 r_dihedral_angle_3_deg 12.15 r_dihedral_angle_1_deg 5.165 r_mcangle_it 1.37 r_angle_refined_deg 1.226 r_mcbond_it 0.884 r_mcbond_other 0.882 r_angle_other_deg 0.714 r_chiral_restr 0.072 r_bond_refined_d 0.01 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 5899 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 60
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing