1W1Z
Structure of the plant like 5-Aminolaevulinic Acid Dehydratase from Chlorobium vibrioforme
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B4K | PDB ENTRY 1B4K |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8.5 | pH 8.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.43 | 72.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 125.235 | α = 90 |
b = 125.235 | β = 90 |
c = 164.603 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 2 |
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 CCD | 2003-10-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 2.6 | 30 | 99.2 | 0.13 | 5.7 | 4.6 | 44567 |
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 | 2.6 | 2.74 | 97.1 | 0.42 | 1.8 | 4.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 ENTRY 1B4K | 2.6 | 8 | 36956 | 1984 | 93.9 | 0.2959 | 0.2905 | 0.3821 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
5401 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_similar_adp_cmpnt | 0.066 |
s_anti_bump_dis_restr | 0.051 |
s_from_restr_planes | 0.0251 |
s_non_zero_chiral_vol | 0.01 |
s_angle_d | 0.006 |
s_zero_chiral_vol | 0.006 |
s_bond_d | 0.002 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4962 |
Nucleic Acid Atoms | |
Solvent Atoms | 325 |
Heterogen Atoms | 16 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELX | refinement |
MOSFLM | data reduction |
SCALED | data scaling |
MOLREP | phasing |