8YHS

The Crystal Structure of BRDT from Biortus.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29318 % PEG 3350, 0.1 M CAPSO 9.0, 17 % PEG 400, 4.8 % 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
2.1437.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.567α = 90
b = 44.38β = 90
c = 72.125γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.00000SPring-8BL45XU

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
11.544.381000.09312.87.818434
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)
11.51.530.879

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.537.7981838391699.9560.1860.18450.221720.51
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]
-1.917-1.6753.592
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.14
r_dihedral_angle_4_deg13.871
r_dihedral_angle_3_deg13.578
r_lrange_it5.755
r_lrange_other5.722
r_dihedral_angle_1_deg5.617
r_scangle_it4.321
r_scangle_other4.319
r_scbond_it2.722
r_scbond_other2.719
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.14
r_dihedral_angle_4_deg13.871
r_dihedral_angle_3_deg13.578
r_lrange_it5.755
r_lrange_other5.722
r_dihedral_angle_1_deg5.617
r_scangle_it4.321
r_scangle_other4.319
r_scbond_it2.722
r_scbond_other2.719
r_mcangle_it2.583
r_mcangle_other2.581
r_mcbond_it1.707
r_mcbond_other1.706
r_angle_refined_deg1.527
r_angle_other_deg1.359
r_nbd_refined0.209
r_nbd_other0.203
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.181
r_symmetry_nbd_refined0.165
r_symmetry_nbd_other0.157
r_symmetry_xyhbond_nbd_refined0.154
r_symmetry_xyhbond_nbd_other0.142
r_chiral_restr0.088
r_symmetry_nbtor_other0.079
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms905
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing