X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OP5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729327.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.5952.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.83α = 90
b = 96.987β = 90
c = 191.67γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96861DiamondI24

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
12.2534.81000.1920.2260.1190.9938.36.781966
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)
12.252.2999.91.1081.3210.7110.6831.76.5

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 REPLACEMENTTHROUGHOUT3OP52.2534.877901398799.950.189770.187570.23289RANDOM35.987
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]
-0.391.78-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.946
r_dihedral_angle_4_deg15.12
r_dihedral_angle_3_deg13.937
r_dihedral_angle_1_deg6.051
r_long_range_B_refined4.739
r_long_range_B_other4.738
r_angle_refined_deg1.231
r_mcangle_it1.116
r_mcangle_other1.116
r_scangle_other0.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.946
r_dihedral_angle_4_deg15.12
r_dihedral_angle_3_deg13.937
r_dihedral_angle_1_deg6.051
r_long_range_B_refined4.739
r_long_range_B_other4.738
r_angle_refined_deg1.231
r_mcangle_it1.116
r_mcangle_other1.116
r_scangle_other0.948
r_angle_other_deg0.775
r_mcbond_it0.605
r_mcbond_other0.605
r_scbond_it0.597
r_scbond_other0.597
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms9905
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing