2B30
Initial Crystallographic Structural Analysis of a putative HAD/COF-like hydrolase from Plasmodium vivax
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1L6R | pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM |
experimental model | PDB | 1NF2 | pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM |
experimental model | PDB | 1NRW | pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM |
experimental model | PDB | 1RKQ | pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM |
experimental model | PDB | 1TJ3 | pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM |
experimental model | PDB | 1RLM | pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 298 | PEG 8000, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.101 | α = 90 |
b = 101.792 | β = 93.93 |
c = 97.337 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | CCD | ADSC QUANTUM 210 | 2005-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.9739 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.7 | 40 | 99.7 | 0.102 | 8.1 | 3.3 | 34235 | 34235 | -3 | 54.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.7 | 2.85 | 99.6 | 0.3 | 3.2 | 3.1 | 4944 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM | 2.7 | 37.24 | 32477 | 32477 | 1726 | 99.5 | 0.20004 | 0.20004 | 0.1968 | 0.25984 | RANDOM | 36.151 |
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] | |
0.03 | 0.03 | -0.05 | 0.03 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.606 |
r_dihedral_angle_4_deg | 18.078 |
r_dihedral_angle_3_deg | 15.17 |
r_dihedral_angle_1_deg | 5.932 |
r_scangle_it | 4.052 |
r_scbond_it | 2.7 |
r_mcangle_it | 2.447 |
r_mcbond_it | 1.577 |
r_angle_refined_deg | 1.104 |
r_angle_other_deg | 0.743 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9054 |
Nucleic Acid Atoms | |
Solvent Atoms | 107 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
PHASER | phasing |