2VKP

Crystal structure of BTB domain from BTBD6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.8M POTASSIUM CITRATE, 0.1M SODIUM CACODYLATE PH6.5
Crystal Properties
Matthews coefficientSolvent content
3.3864

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.135α = 90
b = 58.135β = 90
c = 332.456γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.98248, 0.97874SLSX10SA

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
11.95099.90.0915.86.42775427.91
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)
11.921000.863.86.6

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 DIFFRACTIONSADTHROUGHOUTNONE1.943.0726222140399.80.1960.1940.234RANDOM18.3
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]
1.60.81.6-2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.405
r_dihedral_angle_4_deg20.891
r_dihedral_angle_3_deg11.727
r_scangle_it8.732
r_scbond_it6.877
r_dihedral_angle_1_deg5.22
r_mcangle_it4.796
r_mcbond_it3.662
r_angle_refined_deg1.361
r_angle_other_deg0.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.405
r_dihedral_angle_4_deg20.891
r_dihedral_angle_3_deg11.727
r_scangle_it8.732
r_scbond_it6.877
r_dihedral_angle_1_deg5.22
r_mcangle_it4.796
r_mcbond_it3.662
r_angle_refined_deg1.361
r_angle_other_deg0.889
r_nbd_other0.237
r_symmetry_vdw_refined0.23
r_symmetry_vdw_other0.216
r_nbd_refined0.214
r_symmetry_hbond_refined0.205
r_nbtor_refined0.19
r_xyhbond_nbd_refined0.185
r_nbtor_other0.116
r_chiral_restr0.079
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1625
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing