3F8Z

Human Dihydrofolate Reductase Structural Data with 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, 60% ammonium sulfate, 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.5151.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.416α = 90
b = 84.416β = 90
c = 77.934γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IVmirrors2008-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.6826.2574.80.0710.03916.33.9175932132.56
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)
11.681.77170.2970.2611.31.7590

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 REPLACEMENTTHROUGHOUT1u722.0126.6612126661266670597.020.163510.160550.21877RANDOM19.993
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.318
r_dihedral_angle_3_deg14.986
r_dihedral_angle_4_deg13.625
r_dihedral_angle_1_deg6.329
r_scangle_it3.911
r_scbond_it2.711
r_angle_refined_deg1.969
r_mcangle_it1.645
r_mcbond_it1.073
r_symmetry_hbond_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.318
r_dihedral_angle_3_deg14.986
r_dihedral_angle_4_deg13.625
r_dihedral_angle_1_deg6.329
r_scangle_it3.911
r_scbond_it2.711
r_angle_refined_deg1.969
r_mcangle_it1.645
r_mcbond_it1.073
r_symmetry_hbond_refined0.313
r_nbtor_refined0.304
r_nbd_refined0.219
r_xyhbond_nbd_refined0.213
r_symmetry_vdw_refined0.19
r_chiral_restr0.152
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1497
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms98

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling