X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZKW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.2M NaBr; 0.1M BTP, pH 8.5; 20% Peg 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.921α = 82.21
b = 62.56β = 76.99
c = 67.789γ = 76.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

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
11.5265.5295.40.060.9969.53.5129426
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)
11.521.5594.60.4860.712.33.5

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 REPLACEMENTTHROUGHOUT3ZKW1.5265.52123093633295.330.186540.184830.22129RANDOM25.672
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]
-0.36-1.25-0.080.31.03-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.493
r_dihedral_angle_4_deg21.427
r_dihedral_angle_3_deg13.795
r_long_range_B_refined6.735
r_long_range_B_other6.731
r_dihedral_angle_1_deg6.268
r_scangle_other4.975
r_scbond_it3.633
r_scbond_other3.633
r_mcangle_other3.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.493
r_dihedral_angle_4_deg21.427
r_dihedral_angle_3_deg13.795
r_long_range_B_refined6.735
r_long_range_B_other6.731
r_dihedral_angle_1_deg6.268
r_scangle_other4.975
r_scbond_it3.633
r_scbond_other3.633
r_mcangle_other3.501
r_mcangle_it3.498
r_mcbond_it2.711
r_mcbond_other2.703
r_angle_refined_deg2.338
r_angle_other_deg1.251
r_chiral_restr0.169
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d0.004
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 Atoms6448
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction