3NZB
Structural Analysis of Pneumocystis carinii and Human DHFR Complexes with NADPH and a Series of Potent 5-(omega-carboxyl(alkyloxy)pyrido[2,-d]pyrimidine Derivatives
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CD2 | PDB entry 3cd2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 273 | 33-36% PEG 2K, 46-52 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.86 | α = 90 |
b = 42.709 | β = 94.62 |
c = 60.585 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 200 | CCD | MARMOSAIC 325 mm CCD | mirrors | 2006-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.975 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 1.3 | 50 | 96 | 0.056 | 0.067 | 12.8 | 3.5 | 44341 | 40688 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.3 | 1.37 | 97.7 | 0.645 | 0.759 | 1.7 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3cd2 | 1.45 | 24.66 | 30117 | 30117 | 1629 | 94.79 | 0.24384 | 0.24103 | 0.2954 | RANDOM | 24.031 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.015 |
r_dihedral_angle_4_deg | 16.208 |
r_dihedral_angle_3_deg | 15.479 |
r_dihedral_angle_1_deg | 7.367 |
r_scangle_it | 4.302 |
r_scbond_it | 3.128 |
r_angle_refined_deg | 2.417 |
r_mcangle_it | 2.381 |
r_mcbond_it | 1.492 |
r_symmetry_hbond_refined | 0.537 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1686 |
Nucleic Acid Atoms | |
Solvent Atoms | 73 |
Heterogen Atoms | 114 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |