X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D1I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22912.7 M Na acetate pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.7755.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.168α = 90.15
b = 115.66β = 90.11
c = 115.935γ = 90.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
11.681.9995.70.080.97961.8650665
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)
11.61.6394.10.5881.21.8

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 REPLACEMENTTHROUGHOUT4d1i1.681.996506653284494.530.197770.196890.21403RANDOM24.339
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]
9.471.63-0.25-5.97-1.75-3.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.282
r_dihedral_angle_4_deg19.533
r_dihedral_angle_3_deg13.546
r_dihedral_angle_1_deg7.149
r_long_range_B_refined3.894
r_long_range_B_other3.894
r_scangle_other3.059
r_mcangle_it2.538
r_mcangle_other2.538
r_scbond_it2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.282
r_dihedral_angle_4_deg19.533
r_dihedral_angle_3_deg13.546
r_dihedral_angle_1_deg7.149
r_long_range_B_refined3.894
r_long_range_B_other3.894
r_scangle_other3.059
r_mcangle_it2.538
r_mcangle_other2.538
r_scbond_it2.27
r_scbond_other2.269
r_mcbond_it2.018
r_mcbond_other2.017
r_angle_refined_deg1.927
r_angle_other_deg1.351
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.003
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 Atoms33169
Nucleic Acid Atoms
Solvent Atoms1636
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing