1ZYB

Crystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12734.0M NaFormate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
3.8667.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.98α = 90
b = 115.98β = 90
c = 119.639γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Double-crystal monochromator (Si 111), toroid2005-05-05MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-50.979094, 0.918381SSRLBL1-5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.129.9199.90.0880.0886.46.828282
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1598.80.7660.76614.2

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.1529.225047133299.870.180.1770.228RANDOM38.566
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]
-1.33-0.66-1.331.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.444
r_dihedral_angle_4_deg15.613
r_dihedral_angle_3_deg12.987
r_scangle_it7.474
r_scbond_it5.604
r_dihedral_angle_1_deg5.56
r_mcangle_it3.226
r_mcbond_it2.395
r_angle_refined_deg1.406
r_angle_other_deg0.781
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.444
r_dihedral_angle_4_deg15.613
r_dihedral_angle_3_deg12.987
r_scangle_it7.474
r_scbond_it5.604
r_dihedral_angle_1_deg5.56
r_mcangle_it3.226
r_mcbond_it2.395
r_angle_refined_deg1.406
r_angle_other_deg0.781
r_mcbond_other0.529
r_symmetry_vdw_other0.24
r_symmetry_hbond_refined0.232
r_nbd_refined0.21
r_nbtor_refined0.181
r_symmetry_vdw_refined0.179
r_nbd_other0.173
r_xyhbond_nbd_refined0.143
r_nbtor_other0.085
r_chiral_restr0.084
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1863
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing