3MLE

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529320% PEG3350; 100 MM NH4NO3; 100 MM, BIS-TRIS; 10 MM ATP; 10 MM MGCL2; 10 MM 8-AMINOOCTANOIC ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.773α = 90
b = 131.905β = 90
c = 133.099γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMIRROR2008-07-09MMOLECULAR REPLACEMENT
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9793APS19-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
12.85099.90.0990.09921.6157.73557635576-381.3
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)
12.82.851000.8460.84627.91765

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 REPLACEMENTTHROUGHOUT2QMO2.8503528135281176599.920.2040.2040.2010.246RANDOM59.69
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]
-1.372.76-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.917
r_dihedral_angle_4_deg22.741
r_dihedral_angle_3_deg15.069
r_dihedral_angle_1_deg5.231
r_scangle_it3.98
r_scbond_it2.714
r_mcangle_it2.107
r_mcbond_it1.368
r_angle_refined_deg1.356
r_angle_other_deg1.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.917
r_dihedral_angle_4_deg22.741
r_dihedral_angle_3_deg15.069
r_dihedral_angle_1_deg5.231
r_scangle_it3.98
r_scbond_it2.714
r_mcangle_it2.107
r_mcbond_it1.368
r_angle_refined_deg1.356
r_angle_other_deg1.149
r_mcbond_other0.27
r_chiral_restr0.063
r_bond_refined_d0.014
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10345
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms289

Software

Software
Software NamePurpose
HKL-3000data collection
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000phasing
HKL-2000data reduction
HKL-2000data scaling