3QLZ

Candida glabrata dihydrofolate reductase complexed with NADPH and 5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-propylpyrimidine-2,4-diamine (UCP130B)


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
1.9837.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.607α = 90
b = 42.607β = 90
c = 230.236γ = 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
11.945091.50.1111.64.1276752767533
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)
11.942.0194.10.3194.62826

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 3CSE1.9428.782767527675140091.870.20830.20830.20630.2446RANDOM24.9673
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_deg38.098
r_dihedral_angle_4_deg19.552
r_dihedral_angle_3_deg15.755
r_dihedral_angle_1_deg9.025
r_scangle_it4.083
r_scbond_it2.752
r_mcangle_it1.775
r_mcbond_it1.237
r_angle_refined_deg0.97
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.098
r_dihedral_angle_4_deg19.552
r_dihedral_angle_3_deg15.755
r_dihedral_angle_1_deg9.025
r_scangle_it4.083
r_scbond_it2.752
r_mcangle_it1.775
r_mcbond_it1.237
r_angle_refined_deg0.97
r_nbtor_refined0.315
r_symmetry_vdw_refined0.258
r_nbd_refined0.215
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.137
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3692
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms147

Software

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