X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293.15Reservoir composition: 0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulfate and 0.3 M Sodium nitrate, 0.05 M Tris and 0,05 M BICINE, 12.5 % v/v MPD, 12.5 % w/v PEG1000 and 12.5 % w/v PEG3350 Drop size and composition: sitting drops of 0.3 ul were mixed in a protein:reservoir volume ratio of 3:1 using 45 mg/ml of OtCE15A in 20 mM TRIS pH 8.0
Crystal Properties
Matthews coefficientSolvent content
1.935.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.361α = 75.863
b = 44.263β = 66.326
c = 50.027γ = 70.876
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.3445.4388.90.0920.1010.9956.352.956392514.79
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.341.3788.61.0731.1590.5340.972.93

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6GRW1.3445.431.9463886264589.060.17450.1730.207322.56
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.3092
f_angle_d1.0739
f_chiral_restr0.0749
f_plane_restr0.0086
f_bond_d0.0081
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3074
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms52

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHENIXphasing
XDSdata scaling