3TQ9

Structure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with methotrexate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnliganded CBU_1993

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298100 mM HEPES, pH 7.5 25% PEG 6000 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2445

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.25α = 90
b = 37.193β = 107.66
c = 53.003γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.979NSLSX4C

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
12.310085.90.047193.483297154-3
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)
12.32.34500.1863.53

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTUnliganded CBU_19932.325.738317677636685.870.21810.215630.2659RANDOM73.938
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]
6.741.25-1.48-4.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.673
r_dihedral_angle_3_deg14.606
r_dihedral_angle_4_deg13.149
r_dihedral_angle_1_deg5.424
r_scangle_it1.46
r_angle_refined_deg1.328
r_angle_other_deg0.893
r_scbond_it0.879
r_mcangle_it0.514
r_mcbond_it0.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.673
r_dihedral_angle_3_deg14.606
r_dihedral_angle_4_deg13.149
r_dihedral_angle_1_deg5.424
r_scangle_it1.46
r_angle_refined_deg1.328
r_angle_other_deg0.893
r_scbond_it0.879
r_mcangle_it0.514
r_mcbond_it0.259
r_chiral_restr0.067
r_mcbond_other0.051
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1228
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms81

Software

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