5EXW

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LDNPDB entry 3LDN

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
2.0840.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.682α = 90
b = 74.826β = 98.84
c = 89.658γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-05-06MSINGLE 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 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
11.85188.5931000.0550.0620.02719.14.95740657406
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)
11.921000.1760.1760.0853.658337

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 3LDN1.94054459291099.820.16730.16510.2083RANDOM27.278
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]
0.6-0.93-0.19-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.249
r_dihedral_angle_3_deg11.937
r_dihedral_angle_4_deg11.32
r_dihedral_angle_1_deg5.178
r_mcangle_it1.728
r_angle_refined_deg1.177
r_mcbond_it1.169
r_mcbond_other1.166
r_angle_other_deg0.713
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.249
r_dihedral_angle_3_deg11.937
r_dihedral_angle_4_deg11.32
r_dihedral_angle_1_deg5.178
r_mcangle_it1.728
r_angle_refined_deg1.177
r_mcbond_it1.169
r_mcbond_other1.166
r_angle_other_deg0.713
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms653
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing