3CSE

Candida glabrata Dihydrofolate Reductase complexed with NADPH and 2,4-diamino-5-(3-(2,5-dimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (UCP120B)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.527730 % PEG 4000, 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9938.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.69α = 90
b = 42.69β = 90
c = 230.404γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2007-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
11.65093.20.068124.750325
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)
11.61.6692.70.3862.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.640.0347676255893.220.183430.18080.23171RANDOM25.182
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg35.969
r_dihedral_angle_2_deg35.306
r_dihedral_angle_4_deg19.739
r_dihedral_angle_3_deg14.881
r_scangle_it5.672
r_scbond_it4.124
r_angle_refined_deg2.965
r_mcangle_it2.795
r_mcbond_it2.052
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg35.969
r_dihedral_angle_2_deg35.306
r_dihedral_angle_4_deg19.739
r_dihedral_angle_3_deg14.881
r_scangle_it5.672
r_scbond_it4.124
r_angle_refined_deg2.965
r_mcangle_it2.795
r_mcbond_it2.052
r_nbtor_refined0.321
r_symmetry_hbond_refined0.311
r_chiral_restr0.251
r_nbd_refined0.239
r_symmetry_vdw_refined0.23
r_xyhbond_nbd_refined0.196
r_bond_refined_d0.035
r_gen_planes_refined0.018
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3692
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms142

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction