X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OBI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298Protein 17.6 mg/ml in 0.050 M TRIS-HCL PH 8.0, 0.15 M NACL, 0.005 M TCEP. Reservoir solution 0.1 M MES PH 6.0, 18% (w/v) PEG 3350, 5% (v/v) ethanol. Cryo buffer was reservoir buffer supplemented with 15% glycerol
Crystal Properties
Matthews coefficientSolvent content
1.9135.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.76α = 103.18
b = 35.19β = 112.33
c = 37.82γ = 91.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.0133.9794.70.03614.62.879169
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.011.0385.60.5231.81.51

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 REPLACEMENTTHROUGHOUT2OBI1.0133.9771219374994.70.1150.1140.137RANDOM14.34
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]
-0.960.460.64-0.120.270.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.011
r_sphericity_free16.796
r_dihedral_angle_4_deg16.192
r_dihedral_angle_3_deg14.476
r_sphericity_bonded6.424
r_dihedral_angle_1_deg5.755
r_rigid_bond_restr2.504
r_angle_refined_deg1.877
r_angle_other_deg1.175
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.011
r_sphericity_free16.796
r_dihedral_angle_4_deg16.192
r_dihedral_angle_3_deg14.476
r_sphericity_bonded6.424
r_dihedral_angle_1_deg5.755
r_rigid_bond_restr2.504
r_angle_refined_deg1.877
r_angle_other_deg1.175
r_chiral_restr0.144
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1347
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing