X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DUH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2810.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole
Crystal Properties
Matthews coefficientSolvent content
2.3647.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.587α = 90
b = 68.097β = 90
c = 102.124γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.7656.6691.50.06525.539564
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.821000.194145.7

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 REPLACEMENTTHROUGHOUT4DUH1.7656.6637573189391.260.200050.19880.22414RANDOM31.418
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]
-0.331.02-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_3_deg10.465
r_dihedral_angle_4_deg6.802
r_dihedral_angle_1_deg5.11
r_long_range_B_refined4.367
r_long_range_B_other4.366
r_angle_other_deg3.738
r_scangle_other2.759
r_mcangle_it2.175
r_mcangle_other2.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_3_deg10.465
r_dihedral_angle_4_deg6.802
r_dihedral_angle_1_deg5.11
r_long_range_B_refined4.367
r_long_range_B_other4.366
r_angle_other_deg3.738
r_scangle_other2.759
r_mcangle_it2.175
r_mcangle_other2.175
r_scbond_it1.733
r_scbond_other1.732
r_mcbond_it1.28
r_mcbond_other1.28
r_angle_refined_deg1.255
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_other_d
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 Atoms2843
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing