3QLY

Candida glabrata dihydrofolate reductase complexed with NADPH and 6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP115A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CSEPDB ENTRY 3CSE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277PEG 4000, MgCl2, Tris, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9938.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.731α = 90
b = 42.731β = 90
c = 230.839γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2010-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.100NSLSX25

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
12.5195099.90.1089.25.3137491374933
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)
12.5192.651000.4135.11352

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 3CSE2.51930.22137491374969099.130.21360.21360.21080.2674RANDOM30.9484
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.944
r_dihedral_angle_4_deg16.999
r_dihedral_angle_3_deg13.516
r_dihedral_angle_1_deg5.171
r_scangle_it2.122
r_scbond_it1.322
r_mcangle_it0.976
r_angle_refined_deg0.697
r_mcbond_it0.562
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.944
r_dihedral_angle_4_deg16.999
r_dihedral_angle_3_deg13.516
r_dihedral_angle_1_deg5.171
r_scangle_it2.122
r_scbond_it1.322
r_mcangle_it0.976
r_angle_refined_deg0.697
r_mcbond_it0.562
r_nbtor_refined0.32
r_nbd_refined0.226
r_symmetry_vdw_refined0.2
r_xyhbond_nbd_refined0.135
r_symmetry_hbond_refined0.065
r_chiral_restr0.058
r_gen_planes_refined0.007
r_bond_refined_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3692
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms148

Software

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