X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NXBPDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2OO1PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2OSSPDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2OUOPDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 2RFJPDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental modelPDB 3DAIPDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.227720% PEG10K, 4% Ethylene Glycol, 0.1M HEPES pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3863.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.226α = 90
b = 99.226β = 90
c = 101.137γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-07-13MSINGLE 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
12.2532.7431000.0480.04812.52.81760417604
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)
12.252.371000.4560.45622.82567

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 REPLACEMENTTHROUGHOUTPDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI2.2532.74176101759489299.910.2090.2090.2070.245RANDOM31.265
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]
-0.66-0.33-0.661
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.425
r_dihedral_angle_4_deg22.367
r_dihedral_angle_3_deg14.16
r_scangle_it11.709
r_scbond_it9.302
r_dihedral_angle_1_deg5.605
r_mcangle_it5.521
r_mcbond_it3.906
r_angle_refined_deg1.42
r_mcbond_other1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.425
r_dihedral_angle_4_deg22.367
r_dihedral_angle_3_deg14.16
r_scangle_it11.709
r_scbond_it9.302
r_dihedral_angle_1_deg5.605
r_mcangle_it5.521
r_mcbond_it3.906
r_angle_refined_deg1.42
r_mcbond_other1.25
r_angle_other_deg0.903
r_chiral_restr0.083
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1728
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms1

Software

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