6XG4

X-ray structure of Escherichia coli dihydrofolate reductase L28R mutant in complex with trimethoprim


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherWT DHFR solved in the same space group

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.1 M sodium citrate tribasic dihydrate (pH 5.6), 0.15 M ammonium acetate and 17.5% or 20% PEG 4000; 10 mM NADPH, 2 mM TMP was incubated with the L28R variant of DHFR overnight at 293 K
Crystal Properties
Matthews coefficientSolvent content
3.0359.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.548α = 90
b = 61.548β = 90
c = 104.661γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97919APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.15099.90.0760.025137.59.313880-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.121008.943.0120.6720.78.8

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 REPLACEMENTTHROUGHOUTWT DHFR solved in the same space group2.137.37983770.950.24930.24930.2779FULL CROSS VALIDATION35.198
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]
-0.11-0.05-0.110.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.498
r_dihedral_angle_3_deg18.538
r_dihedral_angle_4_deg13.371
r_dihedral_angle_1_deg7.56
r_angle_refined_deg1.417
r_angle_other_deg1.112
r_chiral_restr0.054
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.498
r_dihedral_angle_3_deg18.538
r_dihedral_angle_4_deg13.371
r_dihedral_angle_1_deg7.56
r_angle_refined_deg1.417
r_angle_other_deg1.112
r_chiral_restr0.054
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1271
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing