3NZ9

Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Five Potent 5-(omega-Carboxy(alkyloxy)Pyrido[2,3-d]pyrimidine Derivatives


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CD2PDB entry 3cd2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627333-336% PEG 2K, 46-52 mM MES pH 6 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
1.9737.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.952α = 90
b = 42.673β = 94.8
c = 60.099γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 325 mm CCDmirrors2006-06-06MSINGLE 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
11.65096.60.0280.04253.624011227792227.9
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)
1.61.6690.30.330.11313.13.22229

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3cd21.824.5122240111610788697.150.205480.201810.27184RANDOM28.375
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.737
r_dihedral_angle_4_deg17.939
r_dihedral_angle_3_deg16.712
r_dihedral_angle_1_deg6.993
r_scangle_it4.847
r_scbond_it3.267
r_mcangle_it2.342
r_angle_refined_deg2.336
r_mcbond_it1.39
r_chiral_restr0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.737
r_dihedral_angle_4_deg17.939
r_dihedral_angle_3_deg16.712
r_dihedral_angle_1_deg6.993
r_scangle_it4.847
r_scbond_it3.267
r_mcangle_it2.342
r_angle_refined_deg2.336
r_mcbond_it1.39
r_chiral_restr0.174
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1686
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms79

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling