X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729220% w/v PEG 3350, 0.2 M NaNO3
Crystal Properties
Matthews coefficientSolvent content
2.7154.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.919α = 90
b = 184.542β = 90.8
c = 183.661γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
11.848.0899.50.0860.1140.0730.99710.44.268238416.9
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)
11.81.8395.80.9831.2960.8370.6721.44.1

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 REPLACEMENTTHROUGHOUT2WVY1.848.086484583386199.460.161090.159840.18522RANDOM27.431
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]
3.93-0.14-1.68-2.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.021
r_dihedral_angle_4_deg14.724
r_dihedral_angle_3_deg12.742
r_dihedral_angle_1_deg6.805
r_long_range_B_refined6.066
r_long_range_B_other6.066
r_scangle_other4.192
r_mcangle_it2.848
r_mcangle_other2.848
r_scbond_it2.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.021
r_dihedral_angle_4_deg14.724
r_dihedral_angle_3_deg12.742
r_dihedral_angle_1_deg6.805
r_long_range_B_refined6.066
r_long_range_B_other6.066
r_scangle_other4.192
r_mcangle_it2.848
r_mcangle_other2.848
r_scbond_it2.811
r_scbond_other2.811
r_mcbond_it2.118
r_mcbond_other2.116
r_angle_refined_deg1.526
r_angle_other_deg0.987
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.008
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 Atoms47560
Nucleic Acid Atoms
Solvent Atoms6759
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing