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Crystal structure of the human 70kDa heat shock protein 5 (BiP/GRP78) ATPase domain in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I33 PDB ENTRY 3I33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 20% PEG 6000, 0.2M CaCl2, 0.1M NaAcetate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.212 α = 98.85 b = 51.795 β = 94.88 c = 94.994 γ = 117.61
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-225 2009-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 2.13 35 94.4 0.13 3.86 44366 41864
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 3I33 2.4 29.12 28620 1506 100 0.19365 0.18965 0.1934 0.26981 0.2727 RANDOM 17.648
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] -0.01 0.01 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.972 r_dihedral_angle_4_deg 18.441 r_dihedral_angle_3_deg 16.79 r_dihedral_angle_1_deg 6.04 r_scangle_it 3.642 r_scbond_it 2.151 r_angle_refined_deg 1.588 r_mcangle_it 1.312 r_angle_other_deg 0.925 r_mcbond_it 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.972 r_dihedral_angle_4_deg 18.441 r_dihedral_angle_3_deg 16.79 r_dihedral_angle_1_deg 6.04 r_scangle_it 3.642 r_scbond_it 2.151 r_angle_refined_deg 1.588 r_mcangle_it 1.312 r_angle_other_deg 0.925 r_mcbond_it 0.69 r_mcbond_other 0.14 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5912 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 58
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling