7TCV

VDAC K12E mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EMN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Tris-HCl, pH 8.5, 10% Polyethylene glycol (PEG) 400 and 16% 2-Methyl-2,4-pentanediol (MPD)
Crystal Properties
Matthews coefficientSolvent content
3.0359.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.197α = 90
b = 57.8β = 97.664
c = 66.44γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
12.649.745990.9918.79.811349
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)
12.62.720.852.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3EMN2.60449.7451134857198.8930.220.21750.220.27660.2854.627
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]
0.585-0.2962.414-2.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.899
r_dihedral_angle_4_deg25.253
r_dihedral_angle_3_deg20.116
r_lrange_other11.911
r_lrange_it11.91
r_scangle_it8.587
r_scangle_other8.584
r_dihedral_angle_1_deg8.031
r_mcangle_other7.038
r_mcangle_it7.036
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2097
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing