3JWM

Crystal structure of Bacillus anthracis dihydrofolate reductase complexed with NADPH and (S)-2,4-diamino-5-(3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-methylpyrimidine (UCP114A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EOBPDB entry 3EOB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.75298Initially grown in 25% PEG 10000, 0.1 M MES. Macroseeding in 10% PEG 10000, 0.1 M MES, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5551.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.884α = 90
b = 77.884β = 90
c = 67.431γ = 90
Symmetry
Space GroupP 42

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152009-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.080900NSLSX29A

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
12.5738.9598.80.0570.05741.97.61215412154-3
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)
12.572.6498.10.1540.15414.37.7898

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 3EOB2.5738.95121541215462298.760.200360.200360.198130.24282RANDOM19.69
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.823
r_dihedral_angle_3_deg17.211
r_dihedral_angle_4_deg16.082
r_dihedral_angle_1_deg5.799
r_scangle_it1.593
r_angle_refined_deg1.264
r_scbond_it1.016
r_mcangle_it0.878
r_mcbond_it0.496
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.823
r_dihedral_angle_3_deg17.211
r_dihedral_angle_4_deg16.082
r_dihedral_angle_1_deg5.799
r_scangle_it1.593
r_angle_refined_deg1.264
r_scbond_it1.016
r_mcangle_it0.878
r_mcbond_it0.496
r_nbtor_refined0.304
r_symmetry_vdw_refined0.206
r_nbd_refined0.183
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.133
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2760
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms148

Software

Software
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling