5EVZ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
2.0740.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.55α = 90
b = 74.802β = 98.6
c = 89.22γ = 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)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
11.825099.90.07713.4564199
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.8599.90.4574.63191

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 REPLACEMENTTHROUGHOUT5EXW1.8544.3158565312099.830.16740.16540.2053RANDOM32.051
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]
1.21-1.12-0.45-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.574
r_dihedral_angle_4_deg15.189
r_dihedral_angle_3_deg11.873
r_dihedral_angle_1_deg5.227
r_mcangle_it1.656
r_angle_refined_deg1.34
r_mcbond_it1.157
r_mcbond_other1.152
r_angle_other_deg0.727
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.574
r_dihedral_angle_4_deg15.189
r_dihedral_angle_3_deg11.873
r_dihedral_angle_1_deg5.227
r_mcangle_it1.656
r_angle_refined_deg1.34
r_mcbond_it1.157
r_mcbond_other1.152
r_angle_other_deg0.727
r_chiral_restr0.071
r_bond_refined_d0.008
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 Atoms5920
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing