7A4U

Crystal structure of lid-truncated apo 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 DROP7.52980.1 M BIS-TRIS propane pH 7.5, 0.2 M trisodium citrate dihydrate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.64647353.55193

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.333α = 90
b = 51.289β = 100.17
c = 119.716γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9760DiamondI24

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
11.7758.9299.90.9759.93.258872
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)
11.771.8199.80.5311.1

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 REPLACEMENTTHROUGHOUT6HAB1.7758.9155912294299.850.18640.18480.217RANDOM32.764
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]
1.54-0.78-1.21-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.735
r_dihedral_angle_4_deg16.508
r_dihedral_angle_3_deg12.177
r_dihedral_angle_1_deg6.638
r_angle_refined_deg1.341
r_angle_other_deg1.263
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.735
r_dihedral_angle_4_deg16.508
r_dihedral_angle_3_deg12.177
r_dihedral_angle_1_deg6.638
r_angle_refined_deg1.341
r_angle_other_deg1.263
r_chiral_restr0.06
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 Atoms3969
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing