X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DWYensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental modelPDB 3DAIensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental modelPDB 3D7Censemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental modelPDB 2OUOensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental modelPDB 2OSSensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental modelPDB 2OO1ensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental modelPDB 2NXBensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC
experimental modelPDB 2GRCensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2M Na_nitrate, 25% w/v PEG 3350, 5% v/v ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4649.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.57α = 90
b = 57.37β = 90
c = 137.3γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5

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
11.7830.83198.90.0790.07918.28.8286192830422.8
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)
11.781.881000.7030.7032.694085

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTensemble of 3DWY, 3DAI, 3D7C, 2OUO, 2OSS, 2OO1, 2NXB, 2GRC1.7829.4528246142898.840.1930.1930.190.237RANDOM15.392
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]
0.45-0.29-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.468
r_dihedral_angle_3_deg14.478
r_dihedral_angle_4_deg13.52
r_scangle_it6.667
r_scbond_it5.21
r_dihedral_angle_1_deg5.187
r_mcangle_it3.557
r_mcbond_it2.808
r_angle_refined_deg1.373
r_mcbond_other1.266
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.468
r_dihedral_angle_3_deg14.478
r_dihedral_angle_4_deg13.52
r_scangle_it6.667
r_scbond_it5.21
r_dihedral_angle_1_deg5.187
r_mcangle_it3.557
r_mcbond_it2.808
r_angle_refined_deg1.373
r_mcbond_other1.266
r_angle_other_deg0.926
r_chiral_restr0.083
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1870
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms20

Software

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