3F8Y

Correlations of Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9287100 mM potassium phosphate, pH 6.9, 30% ammonium sulfate, 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.550.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.294α = 90
b = 84.294β = 90
c = 78.117γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 325 mm CCDmirrors2008-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-11.000SSRLBL9-1

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
11.253.379.40.0390.04616.73504202130.5
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)
11.451.5398.90.1680.5620.91.41654

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1u721.4526.67113454634542181799.130.18980.19170.189780.22762RANDOM19.698
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.298
r_dihedral_angle_3_deg13.631
r_dihedral_angle_4_deg12.798
r_dihedral_angle_1_deg5.898
r_scangle_it2.977
r_scbond_it1.949
r_angle_refined_deg1.802
r_mcangle_it1.365
r_mcbond_it0.823
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.298
r_dihedral_angle_3_deg13.631
r_dihedral_angle_4_deg12.798
r_dihedral_angle_1_deg5.898
r_scangle_it2.977
r_scbond_it1.949
r_angle_refined_deg1.802
r_mcangle_it1.365
r_mcbond_it0.823
r_nbtor_refined0.31
r_nbd_refined0.219
r_xyhbond_nbd_refined0.186
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.145
r_chiral_restr0.125
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms83

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling