X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
Crystal Properties
Matthews coefficientSolvent content
1.830

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.18α = 90
b = 59.661β = 90
c = 88.289γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.337.1970.0818.642.5513628
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.44940.370.861.982.52

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 REPLACEMENTTHROUGHOUT4V2Y2.337.11294067898.750.192280.189290.25008RANDOM42.714
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]
-0.723.54-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.268
r_dihedral_angle_4_deg16.806
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg5.953
r_long_range_B_refined4.751
r_long_range_B_other4.74
r_scangle_other2.788
r_mcangle_it2.019
r_mcangle_other2.018
r_scbond_it1.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.268
r_dihedral_angle_4_deg16.806
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg5.953
r_long_range_B_refined4.751
r_long_range_B_other4.74
r_scangle_other2.788
r_mcangle_it2.019
r_mcangle_other2.018
r_scbond_it1.736
r_scbond_other1.736
r_angle_refined_deg1.463
r_angle_other_deg1.315
r_mcbond_other1.296
r_mcbond_it1.295
r_chiral_restr0.076
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2415
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling