7NAE

Crystal structure of Escherichia coli dihydrofolate reductase in complex with TRIMETHOPRIM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7MYM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277.1518% to 20% PEG4K or 8K, 0.2M Ammonium Sulfate and 2mM DTT
Crystal Properties
Matthews coefficientSolvent content
3.4664.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.542α = 90
b = 65.542β = 90
c = 216.077γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2020-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9795NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.3556.8396.10.0140.020.014130.21.811767
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.431000.1620.2290.1620.96451.8

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 REPLACEMENTTHROUGHOUT7MYM2.3556.831117459396.130.20620.20330.2621RANDOM57.544
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]
0.150.080.15-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.62
r_dihedral_angle_3_deg18.618
r_dihedral_angle_4_deg15.637
r_dihedral_angle_1_deg8.092
r_angle_refined_deg1.615
r_angle_other_deg1.289
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.62
r_dihedral_angle_3_deg18.618
r_dihedral_angle_4_deg15.637
r_dihedral_angle_1_deg8.092
r_angle_refined_deg1.615
r_angle_other_deg1.289
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1267
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms46

Software

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