X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4W4Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M MgCl2, 0.1 M Bis-Tris pH 6.5, 25% PEG 3,350, 3% 1,6-hexanediol
Crystal Properties
Matthews coefficientSolvent content
2.2946.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.137α = 90
b = 84.467β = 93.87
c = 127.894γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2015-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
11.7528.9299.30.0420.99917.93.67882517.1
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)
11.751.7896.50.3163.13.1

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 REPLACEMENTTHROUGHOUT4W4Z1.7528.9274698410399.210.172090.170360.20416RANDOM22.711
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]
-0.13-0.07-0.040.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.31
r_dihedral_angle_4_deg14.852
r_dihedral_angle_3_deg12.03
r_dihedral_angle_1_deg6.63
r_long_range_B_refined6.151
r_long_range_B_other6.151
r_scangle_other2.805
r_mcangle_it2.21
r_mcangle_other2.21
r_scbond_it1.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.31
r_dihedral_angle_4_deg14.852
r_dihedral_angle_3_deg12.03
r_dihedral_angle_1_deg6.63
r_long_range_B_refined6.151
r_long_range_B_other6.151
r_scangle_other2.805
r_mcangle_it2.21
r_mcangle_other2.21
r_scbond_it1.779
r_scbond_other1.779
r_angle_refined_deg1.591
r_angle_other_deg1.322
r_mcbond_other1.321
r_mcbond_it1.32
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms6077
Nucleic Acid Atoms
Solvent Atoms685
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building