X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JKHPDB ENTRY 2JKH

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.946α = 90
b = 74.353β = 90
c = 77.029γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.295099.90.0515.747.2171402-324.9
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)
11.291.3199.80.791.257.08

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JKH1.2940.8865544346696.630.147470.145490.18555RANDOM26.187
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]
-1.130.380.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.254
r_dihedral_angle_4_deg15.84
r_sphericity_free13.344
r_dihedral_angle_3_deg11.234
r_sphericity_bonded11.099
r_dihedral_angle_1_deg6.462
r_rigid_bond_restr2.418
r_angle_refined_deg1.703
r_angle_other_deg0.904
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.254
r_dihedral_angle_4_deg15.84
r_sphericity_free13.344
r_dihedral_angle_3_deg11.234
r_sphericity_bonded11.099
r_dihedral_angle_1_deg6.462
r_rigid_bond_restr2.418
r_angle_refined_deg1.703
r_angle_other_deg0.904
r_chiral_restr0.104
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2251
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
CCP4phasing