2QK8

Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZDRPDB ENTRY: 1ZDR (Bacillus stearothermophilus DHFR)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.697α = 90
b = 41.236β = 119.2
c = 67.032γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator2006-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.258.492.30.09913.73.31686010104232.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2876.80.3422.82.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY: 1ZDR (Bacillus stearothermophilus DHFR)2.4222.87545717137495.680.244220.242730.27382RANDOM44.402
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.162
r_dihedral_angle_4_deg22.184
r_dihedral_angle_3_deg21.543
r_dihedral_angle_1_deg9.67
r_scangle_it3.155
r_scbond_it2.167
r_angle_refined_deg1.895
r_mcangle_it1.725
r_mcbond_it0.959
r_nbtor_refined0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.162
r_dihedral_angle_4_deg22.184
r_dihedral_angle_3_deg21.543
r_dihedral_angle_1_deg9.67
r_scangle_it3.155
r_scbond_it2.167
r_angle_refined_deg1.895
r_mcangle_it1.725
r_mcbond_it0.959
r_nbtor_refined0.335
r_nbd_refined0.281
r_symmetry_vdw_refined0.269
r_symmetry_hbond_refined0.214
r_xyhbond_nbd_refined0.181
r_chiral_restr0.123
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1347
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
BioCARSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing