3QLX

Candida glabrata dihydrofolate reductase complexed with NADPH and 6-methyl-5-[(3R)-3-(3,4,5-trimethoxyphenyl)pent-1-yn-1-yl]pyrimidine-2,4-diamine (UCP112A)


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
2.0138.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.757α = 90
b = 42.757β = 90
c = 232.124γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2009-01-30MSINGLE 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
12.2395099.50.08211.35.2198111981133
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)
12.2392.321000.3375.31946

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 3CSE2.23928.691981119811101799.510.18730.18730.18470.2363RANDOM32.9665
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.206
r_dihedral_angle_4_deg17.338
r_dihedral_angle_3_deg17.28
r_dihedral_angle_1_deg8.861
r_scangle_it4.721
r_scbond_it3.355
r_mcangle_it2.094
r_mcbond_it1.365
r_angle_refined_deg1.121
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.206
r_dihedral_angle_4_deg17.338
r_dihedral_angle_3_deg17.28
r_dihedral_angle_1_deg8.861
r_scangle_it4.721
r_scbond_it3.355
r_mcangle_it2.094
r_mcbond_it1.365
r_angle_refined_deg1.121
r_nbtor_refined0.315
r_symmetry_vdw_refined0.248
r_nbd_refined0.226
r_xyhbond_nbd_refined0.117
r_chiral_restr0.1
r_symmetry_hbond_refined0.077
r_bond_refined_d0.014
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3692
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms148

Software

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