6DO2

Crystal structure of human GRP78 in complex with 7-deaza-2'-C-methyladenosine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29824 to 26% PEG 3350, 0.1 M Tris-HCl and 0.2 M NaCl (by microseeding with the initial crystals from 0.1 M Tris- HCl pH 8.5, 25% PEG 3350 and 0.1 M Na/K tartrate)
Crystal Properties
Matthews coefficientSolvent content
2.1843.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.41α = 90
b = 75.02β = 99.11
c = 89.48γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-06-16LSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.62 - 2.5APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.75099.315.724.4579463
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.724.8979369389899.70.2080.2070.232RANDOM36.63
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]
-7.88414.90233.78184.1024
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5928
Nucleic Acid Atoms
Solvent Atoms354
Heterogen Atoms72

Software

Software
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTERrefinement
XDSdata reduction
BUSTERphasing