X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.12M alcohols (0.02M 1,6-Hexanediol; 0.02M 1-Butanol; 0.02M 1,2-Propanediol; 0.02M 2-Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol), 0.1 M Tris (base)/BICINE pH 8.5, 20% v/v PEG 500* MME; 10 % w/v PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.5551.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.7α = 90
b = 57.7β = 90.1
c = 285.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.98SOLEILPROXIMA 1

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
12.649.499.70.1470.9937.34.755541
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)
12.62.7498.21.210.5760.94.5

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 REPLACEMENTTHROUGHOUT5F7K2.649.455541292499.830.209120.207680.23617RANDOM65.023
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]
1.02-0.770.81-1.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.66
r_dihedral_angle_3_deg18.983
r_dihedral_angle_4_deg10.248
r_long_range_B_refined8.501
r_long_range_B_other8.5
r_dihedral_angle_1_deg7.482
r_scangle_other6.397
r_mcangle_it5.198
r_mcangle_other5.198
r_scbond_it3.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.66
r_dihedral_angle_3_deg18.983
r_dihedral_angle_4_deg10.248
r_long_range_B_refined8.501
r_long_range_B_other8.5
r_dihedral_angle_1_deg7.482
r_scangle_other6.397
r_mcangle_it5.198
r_mcangle_other5.198
r_scbond_it3.931
r_scbond_other3.931
r_mcbond_it3.29
r_mcbond_other3.288
r_angle_refined_deg1.709
r_angle_other_deg0.912
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.003
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 Atoms10952
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing