X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6C5V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729330 % (v/v) Jeffamine ED-2001 pH 7.0 and 0.1 M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4148.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.725α = 90
b = 69.575β = 107.65
c = 93.838γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2018-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
1339.1899.60.2930.3540.1970.9273.23.117505
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)
133.1899.71.0021.2130.6750.4763.1

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 REPLACEMENTTHROUGHOUT6C5V339.181662087399.390.23070.228020.2827RANDOM50.337
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]
0.372.29-4.051.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.345
r_dihedral_angle_4_deg12.411
r_dihedral_angle_3_deg11.843
r_long_range_B_other8.809
r_long_range_B_refined8.808
r_dihedral_angle_1_deg6.639
r_mcangle_it6.042
r_mcangle_other6.042
r_scangle_other5.222
r_mcbond_it3.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.345
r_dihedral_angle_4_deg12.411
r_dihedral_angle_3_deg11.843
r_long_range_B_other8.809
r_long_range_B_refined8.808
r_dihedral_angle_1_deg6.639
r_mcangle_it6.042
r_mcangle_other6.042
r_scangle_other5.222
r_mcbond_it3.554
r_mcbond_other3.553
r_scbond_it3.067
r_scbond_other3.066
r_angle_refined_deg1.346
r_angle_other_deg1.322
r_chiral_restr0.052
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms6395
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction