5F1X

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


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
2.141.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.965α = 90
b = 74.823β = 98.85
c = 90.222γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.944.4799.90.1120.1310.0678.33.85800958009
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)RedundancyNumber Unique Reflections (All)
11.921000.6540.6540.391.13.88461

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 5EXW1.944.4755006294299.710.18320.18090.2279RANDOM31.738
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.098
r_dihedral_angle_3_deg12.752
r_dihedral_angle_4_deg10.448
r_dihedral_angle_1_deg5.212
r_mcangle_it1.939
r_mcbond_it1.314
r_mcbond_other1.313
r_angle_refined_deg1.273
r_angle_other_deg0.746
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.098
r_dihedral_angle_3_deg12.752
r_dihedral_angle_4_deg10.448
r_dihedral_angle_1_deg5.212
r_mcangle_it1.939
r_mcbond_it1.314
r_mcbond_other1.313
r_angle_refined_deg1.273
r_angle_other_deg0.746
r_chiral_restr0.076
r_bond_refined_d0.011
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 Atoms5905
Nucleic Acid Atoms
Solvent Atoms429
Heterogen Atoms62

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing