3DAU

Crystal structure of the ternary MTX NADPH complex of Escherichia coli dihydrofolate reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RH3PDB entry 1RH3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52770.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2161.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.847α = 90
b = 61.847β = 90
c = 104.74γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Bent conical mirror2005-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90000APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.352098.60.05916.75.5559165083311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.498.40.9211.242.95001

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB entry 1RH31.518.88113719935313188698.450.160.1590.186RANDOM26.06
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]
0.10.050.1-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.601
r_dihedral_angle_4_deg14.319
r_sphericity_free13.658
r_dihedral_angle_3_deg13.389
r_sphericity_bonded9.78
r_dihedral_angle_1_deg5.846
r_scangle_it5.287
r_scbond_it4.1
r_mcangle_it2.992
r_rigid_bond_restr2.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.601
r_dihedral_angle_4_deg14.319
r_sphericity_free13.658
r_dihedral_angle_3_deg13.389
r_sphericity_bonded9.78
r_dihedral_angle_1_deg5.846
r_scangle_it5.287
r_scbond_it4.1
r_mcangle_it2.992
r_rigid_bond_restr2.513
r_angle_refined_deg2.219
r_mcbond_it2.212
r_symmetry_vdw_refined0.388
r_nbtor_refined0.31
r_nbd_refined0.207
r_symmetry_hbond_refined0.174
r_chiral_restr0.144
r_xyhbond_nbd_refined0.112
r_bond_refined_d0.022
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1246
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms81

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BioCARSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing