7R6G

Crystal structure of DfrA5 dihydrofolate reductase in complex with TRIMETHOPRIM and NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RX2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277.1523% to 25% PEG3350, 0.1M Mes pH 6.0, 0.3M LiSO4 and 2mM DTT
Crystal Properties
Matthews coefficientSolvent content
3.0259.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.53α = 90
b = 99.53β = 90
c = 42.82γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9795NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.6199.5399.90.170.0740.9717.96.31305735.09
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.612.731000.4970.59126.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RX22.6199.531228074299.630.180.17740.224RANDOM42.102
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]
0.810.81-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.687
r_dihedral_angle_3_deg18.593
r_dihedral_angle_4_deg15.18
r_dihedral_angle_1_deg9.401
r_angle_refined_deg1.89
r_angle_other_deg1.287
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.687
r_dihedral_angle_3_deg18.593
r_dihedral_angle_4_deg15.18
r_dihedral_angle_1_deg9.401
r_angle_refined_deg1.89
r_angle_other_deg1.287
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2470
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing