3I3R
X-ray structure dihydrofolate reductase/thymidylate synthase from babesia bovis at 2.35A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QZF | pdb entry 1QZF modified by the ccp4 program chainsaw |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROFLUDIC MICROBATCH IN A CRYSTAL CARD | 9.5 | 290 | WIZARD SCREEN A1: 20% PEG 8000, 100MM CHES PH 9.5; BABOA.01191.A AT 11.3MG/ML, MICROFLUDIC MICROBATCH IN A CRYSTAL CARD, TEMPERATURE 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.54 | α = 119 |
b = 83.48 | β = 97.99 |
c = 84.19 | γ = 100.69 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | ADSC QUANTUM 315 | 2009-04-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0000 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.35 | 72.2 | 96.8 | 0.099 | 9.64 | 2.9 | 47995 | 47995 | -3 | -3 | 36.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.35 | 2.41 | 96.7 | 0.551 | 2.2 | 2.9 |
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 1QZF modified by the ccp4 program chainsaw | 2.35 | 19.69 | 47995 | 47995 | 2440 | 97.2 | 0.205 | 0.202 | 0.251 | RANDOM | 23.29 |
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] | |
-0.05 | 1.04 | 0.34 | 1.26 | 1.4 | 0.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.08 |
r_dihedral_angle_4_deg | 21.604 |
r_dihedral_angle_3_deg | 14.502 |
r_dihedral_angle_1_deg | 6.815 |
r_scangle_it | 2.056 |
r_scbond_it | 1.26 |
r_angle_refined_deg | 1.191 |
r_mcangle_it | 0.938 |
r_angle_other_deg | 0.843 |
r_mcbond_it | 0.5 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7607 |
Nucleic Acid Atoms | |
Solvent Atoms | 253 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
BOS | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |