7A4V

Crystal structure of lid-truncated ADP-bound BiP in an oligomeric state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HAB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.2 M potassium citrate tribasic monohydrate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.61943353.07245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.179α = 90
b = 51.249β = 99.77
c = 118.801γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9762DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.9429.2799.10.99913.73.343705
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.941.9994.50.7172

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 REPLACEMENTTHROUGHOUT6HAB1.9429.2741507218699.050.1860.18390.2264RANDOM34.398
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]
1.58-0.44-1.35-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.622
r_dihedral_angle_4_deg14.586
r_dihedral_angle_3_deg13.618
r_dihedral_angle_1_deg6.5
r_angle_refined_deg1.333
r_angle_other_deg1.233
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.622
r_dihedral_angle_4_deg14.586
r_dihedral_angle_3_deg13.618
r_dihedral_angle_1_deg6.5
r_angle_refined_deg1.333
r_angle_other_deg1.233
r_chiral_restr0.056
r_bond_refined_d0.006
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 Atoms3937
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing