X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J8F1J8F, 3ZGO
experimental modelPDB 3ZGO1J8F, 3ZGO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 2000
Crystal Properties
Matthews coefficientSolvent content
2.0941.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.186α = 90
b = 142.369β = 94.41
c = 62.626γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

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
11.92098.30.063173.490675

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 REPLACEMENTTHROUGHOUT1J8F, 3ZGO1.92074580390193.60.2330.2310.267RANDOM22.28
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]
0.060.10.15-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.326
r_dihedral_angle_3_deg15.639
r_dihedral_angle_4_deg14.379
r_dihedral_angle_1_deg6.097
r_long_range_B_refined3.183
r_long_range_B_other3.139
r_mcangle_it1.832
r_mcangle_other1.832
r_scangle_other1.816
r_angle_refined_deg1.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.326
r_dihedral_angle_3_deg15.639
r_dihedral_angle_4_deg14.379
r_dihedral_angle_1_deg6.097
r_long_range_B_refined3.183
r_long_range_B_other3.139
r_mcangle_it1.832
r_mcangle_other1.832
r_scangle_other1.816
r_angle_refined_deg1.414
r_scbond_it1.087
r_scbond_other1.087
r_mcbond_it1.078
r_mcbond_other1.077
r_angle_other_deg1.014
r_chiral_restr0.08
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.004
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 Atoms9020
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement