4QJZ

Pneumocystis carinii dihydrofolate reductase ternary complex with NADPH and the inhibitor 24, (N~6~-METHYL-N~6~-(NAPHTHALEN-1-YL)PYRIDO[2,3-D]PYRIMIDINE-2,4,6-TRIAMINE)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IXE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6287ProComplex #11: 0.1 M HEPES, pH 7.5, 25% PEG2KMME, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
238.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.771α = 90
b = 42.813β = 95.28
c = 61.114γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113PIXELDECTRIS PILATUS 6Mmirrors2013-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.975SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.5336.5790.30.080.05682.666138258242224.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.6176.61.650.960.72.13175

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 REPLACEMENTTHROUGHOUT4ixe1.6135.022360722409119895.570.2060.206470.204360.24458RANDOM22.018
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.567
r_dihedral_angle_4_deg16.869
r_dihedral_angle_3_deg16.373
r_dihedral_angle_1_deg6.103
r_angle_refined_deg2.156
r_chiral_restr0.165
r_bond_refined_d0.02
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1686
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms72

Software

Software
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling