3QLR

Candida albicans 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 1AOEPDB ENTRY 1AOE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277PEG 3350, KMES, glycine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1542.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.99α = 90
b = 66.266β = 92.93
c = 75.888γ = 90
Symmetry
Space GroupP 1 21 1

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
12.1495098.80.06719.43.7203752037533
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)
12.1492.19980.1243.71018

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 1AOE2.14937.92037520375104798.730.17890.17890.17550.2441RANDOM21.2418
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_2_deg38.757
r_dihedral_angle_3_deg13.987
r_dihedral_angle_4_deg13.307
r_dihedral_angle_1_deg6.081
r_scangle_it2.065
r_scbond_it1.408
r_angle_refined_deg1.324
r_mcangle_it1.019
r_mcbond_it0.599
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.757
r_dihedral_angle_3_deg13.987
r_dihedral_angle_4_deg13.307
r_dihedral_angle_1_deg6.081
r_scangle_it2.065
r_scbond_it1.408
r_angle_refined_deg1.324
r_mcangle_it1.019
r_mcbond_it0.599
r_nbtor_refined0.302
r_nbd_refined0.192
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.14
r_xyhbond_nbd_refined0.127
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3128
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms170

Software

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