3JVX

Crystal structure of Bacillus anthracis dihydrofolate reductase complexed with NADPH and 2,4-diamino-5-(3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (UCP120A)


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
2.5551.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.241α = 90
b = 78.241β = 90
c = 66.79γ = 90
Symmetry
Space GroupP 42

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDADSC QUANTUM 3152008-08-17MSINGLE 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
12.2528.5999.910.1420.14212.66.61829918299-3
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)
12.252.3199.370.5120.51236.5989

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 3EOB2.2528.59182991829998999.910.181630.181630.180230.20764RANDOM27.466
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_deg36.374
r_dihedral_angle_4_deg18.528
r_dihedral_angle_3_deg14.125
r_dihedral_angle_1_deg6.057
r_scangle_it2.323
r_scbond_it1.453
r_angle_refined_deg1.323
r_mcangle_it1.072
r_mcbond_it0.62
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.374
r_dihedral_angle_4_deg18.528
r_dihedral_angle_3_deg14.125
r_dihedral_angle_1_deg6.057
r_scangle_it2.323
r_scbond_it1.453
r_angle_refined_deg1.323
r_mcangle_it1.072
r_mcbond_it0.62
r_nbtor_refined0.306
r_symmetry_vdw_refined0.216
r_nbd_refined0.18
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.138
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2780
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms146

Software

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