5F2R

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


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
2.0239.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.958α = 90
b = 74.549β = 98.15
c = 88.414γ = 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
12.115099.30.1329.3440808
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)
12.112.1595.90.4093.11947

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 5EXW2.154436420194099.320.20050.19870.2344RANDOM35.688
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]
1.56-1.29-1.08-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.57
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg12.865
r_dihedral_angle_1_deg5.299
r_mcangle_it2.033
r_mcbond_it1.338
r_mcbond_other1.338
r_angle_refined_deg1.274
r_angle_other_deg0.888
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.57
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg12.865
r_dihedral_angle_1_deg5.299
r_mcangle_it2.033
r_mcbond_it1.338
r_mcbond_other1.338
r_angle_refined_deg1.274
r_angle_other_deg0.888
r_chiral_restr0.075
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5900
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms64

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing