X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527730% Jeffamine600, 0.5M CsCl, 5% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2545.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.6α = 90
b = 71.71β = 90
c = 31.97γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.542

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
11.6129.1699.50.0550.05516.13.4162951621314
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)
11.611.7970.240.242.63.12248

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 3HMH, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY1.6129.16162721617182999.380.15020.15020.14850.1837RANDOM13.0347
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]
-0.14-0.250.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.108
r_dihedral_angle_4_deg21.234
r_dihedral_angle_3_deg11.254
r_scangle_it6.729
r_dihedral_angle_1_deg5.061
r_scbond_it4.754
r_mcangle_it2.905
r_mcbond_it1.739
r_angle_refined_deg1.724
r_angle_other_deg1.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.108
r_dihedral_angle_4_deg21.234
r_dihedral_angle_3_deg11.254
r_scangle_it6.729
r_dihedral_angle_1_deg5.061
r_scbond_it4.754
r_mcangle_it2.905
r_mcbond_it1.739
r_angle_refined_deg1.724
r_angle_other_deg1.529
r_mcbond_other0.528
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms903
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms41

Software

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