3NZD

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U72PDB entry 1u72

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9287100 mM KPO4, 30% saturated ammonium sulfate, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.550.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.622α = 90
b = 84.622β = 90
c = 77.597γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 325 mm CCDmirrors2008-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.975SSRLBL9-2

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
11.853.395.30.0620.073153.723216183152228.4
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)
1.81.974.20.3420.4043.33.22090

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 1u721.853.322232161736694795.270.166740.16340.23163RANDOM19.949
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_deg36.468
r_dihedral_angle_3_deg15.402
r_dihedral_angle_4_deg13.519
r_dihedral_angle_1_deg6.491
r_scangle_it5.158
r_scbond_it3.384
r_angle_refined_deg2.231
r_mcangle_it2.133
r_mcbond_it1.238
r_chiral_restr0.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.468
r_dihedral_angle_3_deg15.402
r_dihedral_angle_4_deg13.519
r_dihedral_angle_1_deg6.491
r_scangle_it5.158
r_scbond_it3.384
r_angle_refined_deg2.231
r_mcangle_it2.133
r_mcbond_it1.238
r_chiral_restr0.329
r_bond_refined_d0.025
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms80

Software

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