X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OCX5OCX (early model)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629320% (w/v) PEG 6000, 0.1 M MES pH 6.0, 0.2 M ammonium chloride
Crystal Properties
Matthews coefficientSolvent content
1.9937.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.91α = 90
b = 62.05β = 90
c = 124.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.834.399.90.0510.02150.99923.36.64003117.5
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)
11.81.8641000.2180.0910.97586.7

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 REPLACEMENTTHROUGHOUT5OCX (early model)1.834.338055197799.860.172310.17020.21339RANDOM21.041
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]
-0.470.220.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.749
r_dihedral_angle_4_deg14.723
r_dihedral_angle_3_deg11.127
r_dihedral_angle_1_deg6.592
r_long_range_B_refined4.994
r_long_range_B_other4.686
r_angle_refined_deg1.459
r_mcangle_it1.136
r_mcangle_other1.136
r_scangle_other1.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.749
r_dihedral_angle_4_deg14.723
r_dihedral_angle_3_deg11.127
r_dihedral_angle_1_deg6.592
r_long_range_B_refined4.994
r_long_range_B_other4.686
r_angle_refined_deg1.459
r_mcangle_it1.136
r_mcangle_other1.136
r_scangle_other1.052
r_angle_other_deg0.936
r_scbond_it0.646
r_scbond_other0.646
r_mcbond_it0.632
r_mcbond_other0.632
r_chiral_restr0.086
r_bond_refined_d0.01
r_bond_other_d0.007
r_gen_planes_refined0.006
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 Atoms3234
Nucleic Acid Atoms
Solvent Atoms436
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing