3QXC

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ATP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529320% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; 5% GLYCEROL; 10 MM 8-AMINOOCTANOIC ACID; SOAKED WITH 10 MM ATP, 10 MM MGCL2; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
1.9336.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.883α = 90
b = 37.691β = 101.24
c = 69.184γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3MIRROR2008-07-12MMOLECULAR REPLACEMENT
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97857APS19-BM

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
11.345098.10.040.0435.13.64581945819-317.2
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)
11.341.3683.50.40.42.22.51964

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2QMO1.34504346443464231997.850.14020.14020.138460.17281RANDOM13.683
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]
-0.45-0.220.69-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.823
r_dihedral_angle_4_deg18.344
r_dihedral_angle_3_deg11.429
r_dihedral_angle_1_deg6.38
r_scangle_it5.909
r_scbond_it4.448
r_mcangle_it3.375
r_rigid_bond_restr2.95
r_mcbond_it2.705
r_mcbond_other2.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.823
r_dihedral_angle_4_deg18.344
r_dihedral_angle_3_deg11.429
r_dihedral_angle_1_deg6.38
r_scangle_it5.909
r_scbond_it4.448
r_mcangle_it3.375
r_rigid_bond_restr2.95
r_mcbond_it2.705
r_mcbond_other2.586
r_angle_refined_deg2.033
r_angle_other_deg1.223
r_chiral_restr0.152
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.004
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1754
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms97

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling