X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2810.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole
Crystal Properties
Matthews coefficientSolvent content
2.3748.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.882α = 90
b = 67.75β = 90
c = 102.96γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-07-08MSINGLE 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
11.7367.7595.30.04916.54.543503
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)
11.731.770.523

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 REPLACEMENTTHROUGHOUT4DUH1.7356.6641311209994.540.197880.196440.22665RANDOM30.584
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]
0.270.32-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.84
r_dihedral_angle_3_deg12.502
r_dihedral_angle_4_deg7.073
r_long_range_B_other6.362
r_long_range_B_refined6.361
r_scangle_other5.757
r_dihedral_angle_1_deg5.372
r_scbond_it4.512
r_scbond_other4.51
r_mcangle_other4.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.84
r_dihedral_angle_3_deg12.502
r_dihedral_angle_4_deg7.073
r_long_range_B_other6.362
r_long_range_B_refined6.361
r_scangle_other5.757
r_dihedral_angle_1_deg5.372
r_scbond_it4.512
r_scbond_other4.51
r_mcangle_other4.015
r_mcangle_it4.013
r_angle_other_deg3.528
r_mcbond_it3.37
r_mcbond_other3.355
r_angle_refined_deg1.187
r_chiral_restr0.052
r_bond_refined_d0.007
r_gen_planes_other0.005
r_gen_planes_refined0.004
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 Atoms2875
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms63

Software

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