X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OK7PDB ENTRY 2OK7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch, permeable oil6.529312% PEG 6000, 5% glycerol, 0.1 M cacodylate-NaOH , pH 6.5, Microbatch, permeable oil, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5952.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.57α = 90
b = 122.57β = 90
c = 133.744γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-10-07
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.856.581000.1579.53.94499444994
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
33.1699.90.7751.73.76554

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 ENTRY 2OK7356.5824269342693226899.960.247760.247760.244150.31661RANDOM55.833
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]
2.31.152.3-3.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.118
r_dihedral_angle_3_deg17.982
r_dihedral_angle_4_deg17.865
r_dihedral_angle_1_deg5.575
r_scangle_it2.773
r_mcangle_it1.914
r_scbond_it1.645
r_angle_refined_deg1.332
r_mcbond_it1.061
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.118
r_dihedral_angle_3_deg17.982
r_dihedral_angle_4_deg17.865
r_dihedral_angle_1_deg5.575
r_scangle_it2.773
r_mcangle_it1.914
r_scbond_it1.645
r_angle_refined_deg1.332
r_mcbond_it1.061
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13228
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms480

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling