3L3R

Structural, Computational and Kinetic Data for Antifolate Interactions Against Pneumocystis jirovecii, Pneumocystis carinii and Human Dihydrofolate Reductase and Their Active Site Mutants


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U72 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.928060-64% saturate ammonium sufate, 3% ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.5351.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.53α = 90
b = 84.53β = 90
c = 78.423γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54118

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
1226.197.80.180.114.44.321070133502115
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)
122.199.90.90.0114.642070

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT1U72226.12141321267766894.520.1780.174610.170570.25711RANDOM22.161
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.362
r_dihedral_angle_4_deg16.576
r_dihedral_angle_3_deg16.557
r_dihedral_angle_1_deg6.676
r_scangle_it4.956
r_scbond_it3.319
r_angle_refined_deg2.342
r_mcangle_it2.027
r_mcbond_it1.183
r_chiral_restr0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.362
r_dihedral_angle_4_deg16.576
r_dihedral_angle_3_deg16.557
r_dihedral_angle_1_deg6.676
r_scangle_it4.956
r_scbond_it3.319
r_angle_refined_deg2.342
r_mcangle_it2.027
r_mcbond_it1.183
r_chiral_restr0.23
r_bond_refined_d0.025
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms75

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling