3EIG

Crystal structure of a methotrexate-resistant mutant of human dihydrofolate reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U72PDB ENTRY 1U72

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.2 M sodium dihydrogen phosphate, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1542.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.348α = 90
b = 47.868β = 90
c = 90.715γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++Osmic Confocal Blue2008-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.75097.20.0640.06414.611.7204612046121.584801
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7693.90.4730.4739.51941

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1U721.710.522030420304206697.260.179290.179290.174420.22297RANDOM16.372
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]
-0.13-0.070.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.599
r_dihedral_angle_4_deg20.37
r_dihedral_angle_3_deg11.879
r_dihedral_angle_1_deg6.074
r_scangle_it2.591
r_scbond_it1.73
r_angle_refined_deg1.417
r_mcangle_it1.081
r_mcbond_it0.736
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.599
r_dihedral_angle_4_deg20.37
r_dihedral_angle_3_deg11.879
r_dihedral_angle_1_deg6.074
r_scangle_it2.591
r_scbond_it1.73
r_angle_refined_deg1.417
r_mcangle_it1.081
r_mcbond_it0.736
r_nbtor_refined0.307
r_symmetry_vdw_refined0.224
r_nbd_refined0.209
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.136
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1464
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms74

Software

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