3NZA

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 DROP627333-36% PEG 2K, 46-52 mM MES pH 6.0, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
1.9938.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.959α = 90
b = 42.679β = 94.57
c = 60.609γ = 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
11.760.597.50.070.0644.42.521070194462229.7
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)
1.71.76980.3760.32514.121144

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 3cd21.927.8922210701388474997.350.210010.205920.28178RANDOM28.354
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_deg30.431
r_dihedral_angle_3_deg18.034
r_dihedral_angle_4_deg16.016
r_dihedral_angle_1_deg8.578
r_scangle_it4.767
r_scbond_it3.076
r_angle_refined_deg2.299
r_mcangle_it2.236
r_mcbond_it1.323
r_chiral_restr0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.431
r_dihedral_angle_3_deg18.034
r_dihedral_angle_4_deg16.016
r_dihedral_angle_1_deg8.578
r_scangle_it4.767
r_scbond_it3.076
r_angle_refined_deg2.299
r_mcangle_it2.236
r_mcbond_it1.323
r_chiral_restr0.16
r_bond_refined_d0.022
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1686
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms80

Software

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