5EX5

Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 7-deaza-ADP and inorganic phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EXWPDB entry 5EXW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528924-26% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride
Crystal Properties
Matthews coefficientSolvent content
2.0439.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.27α = 90
b = 74.709β = 98.38
c = 88.722γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.94099.10.1170.1170.1340.0640.9939.34.25583155831
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)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9299.10.5020.0560.0310.8383.34.28075

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 5EXW1.937.8752967282498.90.17290.17080.2122RANDOM25.438
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]
1-1.1-0.15-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.734
r_dihedral_angle_4_deg15.682
r_dihedral_angle_3_deg12.354
r_dihedral_angle_1_deg5.172
r_mcangle_it1.635
r_angle_refined_deg1.286
r_mcbond_it1.091
r_mcbond_other1.09
r_angle_other_deg0.712
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.734
r_dihedral_angle_4_deg15.682
r_dihedral_angle_3_deg12.354
r_dihedral_angle_1_deg5.172
r_mcangle_it1.635
r_angle_refined_deg1.286
r_mcbond_it1.091
r_mcbond_other1.09
r_angle_other_deg0.712
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5908
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing