X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NXBEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OO1Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OSSEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OUOEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2RFJEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DAIEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3D7CEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DWYEnsemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52770.1M NaOAc.3H20 pH 5.5, 1.1M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4349.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.39α = 90
b = 81.39β = 90
c = 79.475γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
12.236.2211000.0740.07414.48152661526650.8
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)
12.22.321000.7440.74424.32231

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 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY2.236.22152521523874499.910.2270.2270.2240.27RANDOM33.606
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]
1.740.871.74-2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.303
r_dihedral_angle_3_deg17.828
r_dihedral_angle_4_deg14.163
r_scangle_it6.463
r_dihedral_angle_1_deg6.042
r_scbond_it6.027
r_mcangle_it3.826
r_mcbond_it3.105
r_mcbond_other2.051
r_angle_refined_deg1.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.303
r_dihedral_angle_3_deg17.828
r_dihedral_angle_4_deg14.163
r_scangle_it6.463
r_dihedral_angle_1_deg6.042
r_scbond_it6.027
r_mcangle_it3.826
r_mcbond_it3.105
r_mcbond_other2.051
r_angle_refined_deg1.459
r_angle_other_deg0.94
r_chiral_restr0.094
r_bond_refined_d0.016
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 Atoms1891
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms12

Software

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