X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I15 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527720% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6854

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.621α = 90
b = 115.344β = 108.32
c = 68.585γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2016-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97622DiamondI03

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
11.94265.1193.30.1060.1270.0690.9919.23.358668
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)
11.9421.97696.30.8631.0260.550.662.13.4

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 REPLACEMENTTHROUGHOUT4I151.94265.1155658294493.220.181260.178940.22457RANDOM30.539
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]
3.83-1.19-0.38-2.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.269
r_dihedral_angle_4_deg15.122
r_dihedral_angle_3_deg14.869
r_long_range_B_refined6.641
r_long_range_B_other6.614
r_dihedral_angle_1_deg5.921
r_scangle_other4.668
r_mcangle_it3.44
r_mcangle_other3.44
r_scbond_it3.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.269
r_dihedral_angle_4_deg15.122
r_dihedral_angle_3_deg14.869
r_long_range_B_refined6.641
r_long_range_B_other6.614
r_dihedral_angle_1_deg5.921
r_scangle_other4.668
r_mcangle_it3.44
r_mcangle_other3.44
r_scbond_it3.05
r_scbond_other3.049
r_mcbond_it2.253
r_mcbond_other2.252
r_angle_refined_deg1.5
r_angle_other_deg1.363
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms5260
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building