X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WVY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.429218% (w/v) PEG 3350, 0.1 M Bis-Tris propane, pH 6.4, 0.2 M NaBr
Crystal Properties
Matthews coefficientSolvent content
4.0869.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 272.301α = 90
b = 272.301β = 90
c = 190.047γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.549.6799.80.210.2180.060.99818.62514217133.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5496.722.090.5790.7352.224.5

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 REPLACEMENTTHROUGHOUT2WVY2.549.67135113701199.770.18260.180560.22176RANDOM50.745
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]
1.120.561.12-3.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.164
r_dihedral_angle_4_deg18.687
r_dihedral_angle_3_deg14.634
r_dihedral_angle_1_deg6.486
r_long_range_B_refined6.107
r_long_range_B_other6.107
r_mcangle_it4.048
r_mcangle_other4.048
r_scangle_other3.725
r_mcbond_it2.532
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.164
r_dihedral_angle_4_deg18.687
r_dihedral_angle_3_deg14.634
r_dihedral_angle_1_deg6.486
r_long_range_B_refined6.107
r_long_range_B_other6.107
r_mcangle_it4.048
r_mcangle_other4.048
r_scangle_other3.725
r_mcbond_it2.532
r_mcbond_other2.528
r_scbond_it2.282
r_scbond_other2.282
r_angle_refined_deg1.318
r_angle_other_deg0.961
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms16609
Nucleic Acid Atoms
Solvent Atoms1293
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing