X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP300PEG 1500, Glycerol

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.861α = 90
b = 40.578β = 108.62
c = 115.449γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2012-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.0Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.185098.817.62.619873
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.182.22

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 REPLACEMENTTHROUGHOUT5ZHF2.18301887898898.660.161420.159060.20755RANDOM37.626
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]
0.410.31-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.024
r_dihedral_angle_4_deg17.504
r_dihedral_angle_3_deg12.719
r_long_range_B_refined6.536
r_long_range_B_other6.535
r_dihedral_angle_1_deg5.712
r_scangle_other4.953
r_mcangle_it3.546
r_mcangle_other3.546
r_scbond_it3.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.024
r_dihedral_angle_4_deg17.504
r_dihedral_angle_3_deg12.719
r_long_range_B_refined6.536
r_long_range_B_other6.535
r_dihedral_angle_1_deg5.712
r_scangle_other4.953
r_mcangle_it3.546
r_mcangle_other3.546
r_scbond_it3.153
r_scbond_other3.152
r_mcbond_it2.273
r_mcbond_other2.27
r_angle_refined_deg1.339
r_angle_other_deg0.946
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.006
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
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2924
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEmodel building