X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F7K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2- Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M Buffer System 2 (Sodium HEPES; MOPS (acid)) pH 7.5, 50 % v/v EDO_P8K (40% v/v Ethylene glycol; 20 % w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.2261.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.9α = 90
b = 134.91β = 102.52
c = 123.8γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.6267.4699.80.1139.65.698949
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.622.7699.95.82.8

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 REPLACEMENTTHROUGHOUT5F7K2.6267.4694042487899.80.190570.188170.23688RANDOM64.988
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]
0.63-1-0.840.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.479
r_dihedral_angle_4_deg23.765
r_dihedral_angle_3_deg17.205
r_long_range_B_refined7.494
r_long_range_B_other7.493
r_dihedral_angle_1_deg6.78
r_scangle_other5.635
r_mcangle_it4.829
r_mcangle_other4.829
r_scbond_it3.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.479
r_dihedral_angle_4_deg23.765
r_dihedral_angle_3_deg17.205
r_long_range_B_refined7.494
r_long_range_B_other7.493
r_dihedral_angle_1_deg6.78
r_scangle_other5.635
r_mcangle_it4.829
r_mcangle_other4.829
r_scbond_it3.554
r_scbond_other3.554
r_mcbond_it3.031
r_mcbond_other3.03
r_angle_refined_deg1.677
r_angle_other_deg0.898
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms16268
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms288

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing