X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2YPDB ENTRY 4V2Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1100 MM TRI-SODIUM CITRATE PH 5.6, 1.0 M AMMONIUM PHOSPHATE
Crystal Properties
Matthews coefficientSolvent content
1.830

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.35α = 90
b = 59.43β = 90
c = 86.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-02-12MSINGLE 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
11.7537.297.70.079.792.8630163-3
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)
11.751.8696.50.482.162.79

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 4V2Y1.7537.2428637151299.440.15670.154950.19053RANDOM31.362
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]
-2.050.791.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.82
r_dihedral_angle_4_deg12.987
r_dihedral_angle_3_deg12.896
r_dihedral_angle_1_deg6.437
r_scbond_it2.609
r_angle_refined_deg2.397
r_mcangle_it2.179
r_mcbond_it1.381
r_mcbond_other1.38
r_angle_other_deg1.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.82
r_dihedral_angle_4_deg12.987
r_dihedral_angle_3_deg12.896
r_dihedral_angle_1_deg6.437
r_scbond_it2.609
r_angle_refined_deg2.397
r_mcangle_it2.179
r_mcbond_it1.381
r_mcbond_other1.38
r_angle_other_deg1.163
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2186
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling