1ZS7
The structure of gene product APE0525 from Aeropyrum pernix
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.9 | 293 | K/Na Phosphate, glycerol, ethylene glycol, sucrose, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.85 | α = 90 |
b = 112.792 | β = 90 |
c = 39.001 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 105 | CCD | CUSTOM-MADE | 2004-12-14 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97940, 0.97959 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.85 | 36.9 | 94.4 | 0.079 | 17.2 | 4.5 | 19171 | 19171 |
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) | |||||||||||
1 | 1.85 | 1.92 | 79.9 | 0.434 | 2.1 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.85 | 36.86 | 18045 | 17112 | 933 | 94.44 | 0.1683 | 0.1683 | 0.16668 | 0.19883 | RANDOM | 19.906 |
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] | |
0.45 | -0.15 | -0.3 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 22.94 |
r_dihedral_angle_4_deg | 15.492 |
r_dihedral_angle_3_deg | 12.873 |
r_dihedral_angle_1_deg | 5.553 |
r_scangle_it | 3.865 |
r_scbond_it | 2.35 |
r_angle_refined_deg | 1.287 |
r_mcangle_it | 1.24 |
r_mcbond_it | 0.644 |
r_nbtor_refined | 0.297 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1470 |
Nucleic Acid Atoms | |
Solvent Atoms | 246 |
Heterogen Atoms | 26 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-2000 | data scaling |
HKL-3000 | phasing |
SHELXD | phasing |
SHELXE | model building |
MLPHARE | phasing |
DM | phasing |
SOLVE | phasing |
RESOLVE | phasing |
O | model building |
Coot | model building |
CCP4 | phasing |
ARP/wARP | model building |