X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H9U6H9U, 2W51
experimental modelPDB 2W516H9U, 2W51

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2937% PEG6000, 0.1 M Tris-HCl pH7.5
Crystal Properties
Matthews coefficientSolvent content
2.754.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.42α = 81.13
b = 60.96β = 88.33
c = 96.11γ = 74.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.916DiamondI04-1

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
12.4936.5298.10.050.0720.050.99913.33.543348
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)
12.492.5598.10.7070.9990.7070.6171.63.6

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 REPLACEMENTTHROUGHOUT6H9U, 2W512.4936.5241261208598.090.227820.226360.25608RANDOM68.258
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]
1.67-1.18-0.53-2.37-0.550.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.83
r_dihedral_angle_4_deg13.941
r_dihedral_angle_3_deg13.654
r_dihedral_angle_1_deg5.303
r_long_range_B_refined2.061
r_long_range_B_other2.061
r_mcangle_it1.326
r_mcangle_other1.326
r_scangle_other1.175
r_angle_refined_deg0.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.83
r_dihedral_angle_4_deg13.941
r_dihedral_angle_3_deg13.654
r_dihedral_angle_1_deg5.303
r_long_range_B_refined2.061
r_long_range_B_other2.061
r_mcangle_it1.326
r_mcangle_other1.326
r_scangle_other1.175
r_angle_refined_deg0.794
r_mcbond_it0.756
r_mcbond_other0.756
r_angle_other_deg0.686
r_scbond_it0.665
r_scbond_other0.665
r_chiral_restr0.033
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms8214
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing