X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5O6H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62910.4M Sodium phosphate buffer, 17.5% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2946.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.918α = 90
b = 177.285β = 90
c = 58.298γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-05-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.458098.60.0670.0430.99815.26.514511212.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4796.60.8140.5570.7662.15.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5O6H1.4580136923722797.830.215020.213460.24416RANDOM20.092
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]
2.56-0.81-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.884
r_dihedral_angle_4_deg21.128
r_dihedral_angle_3_deg15.099
r_dihedral_angle_1_deg6.336
r_long_range_B_refined5.422
r_scbond_it2.694
r_mcangle_it2.622
r_angle_refined_deg2.351
r_mcbond_it1.951
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.884
r_dihedral_angle_4_deg21.128
r_dihedral_angle_3_deg15.099
r_dihedral_angle_1_deg6.336
r_long_range_B_refined5.422
r_scbond_it2.694
r_mcangle_it2.622
r_angle_refined_deg2.351
r_mcbond_it1.951
r_chiral_restr0.163
r_bond_refined_d0.024
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6281
Nucleic Acid Atoms
Solvent Atoms820
Heterogen Atoms222

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing