X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DVVEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 1X0JEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 3DAIEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 3HMHEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 2GRCEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 2OO1Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 2OSSEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 2OUOEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 3D7CEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY
experimental modelPDB 3DWYEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.827720% PEG3350 0.1 M bis tris propane, 10% ethylene glycol 0.15 M sodium nitrate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4850.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.835α = 90
b = 60.835β = 90
c = 63.679γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2013-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.651999.70.0260.02640.16.7168431679320.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7498.30.1350.1355.85.52379

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTEnsemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY1.6519168381676784799.580.17670.17670.17440.2198RANDOM25.5295
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]
-0.19-0.19-0.190.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.042
r_dihedral_angle_4_deg18.127
r_dihedral_angle_3_deg13.125
r_mcangle_it5.662
r_mcbond_it4.922
r_dihedral_angle_1_deg4.755
r_mcbond_other4.651
r_angle_refined_deg1.615
r_angle_other_deg0.883
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.042
r_dihedral_angle_4_deg18.127
r_dihedral_angle_3_deg13.125
r_mcangle_it5.662
r_mcbond_it4.922
r_dihedral_angle_1_deg4.755
r_mcbond_other4.651
r_angle_refined_deg1.615
r_angle_other_deg0.883
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms936
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms8

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction