4L0U
Crystal structure of Plasmodium vivax Prx1a
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2H66 | PDB ENTRY 2H66 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.6 | 300 | 1.5 uL of 8 mg/mL protein in 10 mM HEPES pH 7.5 500 mM NaCl + 1.5 uL reservoir solution 5% PEG 4000, 50 mM NaAc, 100 mM NaAc, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.55 | α = 90 |
b = 149.59 | β = 104.88 |
c = 131.91 | 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 | 100 | CCD | ADSC QUANTUM 210 | 2006-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | APS | 17-ID |
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 | 2.48 | 41.56 | 99.2 | 0.115 | 0.098 | 10.8 | 3.4 | 86441 | 57.77 |
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) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.48 | 2.53 | 99.8 | 0.488 | 0.498 | 1.3 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 2H66 | 2.5 | 40.25 | 86438 | 4302 | 0.178 | 0.176 | 0.212 | RANDOM | 54.4 |
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] | |
1.825 | -3.2364 | -3.9052 | 2.0802 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.14 |
t_omega_torsion | 3.46 |
t_angle_deg | 1.1 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13476 |
Nucleic Acid Atoms | |
Solvent Atoms | 260 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
BUSTER | refinement |
ADSC | data collection |
HKL-2000 | data scaling |