1RU2
CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E.COLI HPPK(V83G/DEL84-89) WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN AT 1.48 ANGSTROM RESOLUTION (ORTHORHOMBIC FORM)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Q0N | PDB ID 1Q0N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 292 | PEG4000, MAGNESIUM CHLORIDE, ACETATE, GLYCEROL, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.73 | 28.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.609 | α = 90 |
b = 63.156 | β = 90 |
c = 36.201 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 QUANTUM 4 | MIRROR | 2001-07-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X9B | 1.00928 | NSLS | X9B |
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 | 1.48 | 30 | 99.8 | 0.132 | 14.6166 | 7.414 | 20535 | 20535 | 25.3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.48 | 1.53 | 99.9 | 0.599 | 1.884 | 6.31 | 1993 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | FREE R | PDB ID 1Q0N | 1.48 | 30 | 2 | 4 | 19335 | 15068 | 1015 | 94.9 | 0.172 | 0.158 | 0.164 | 0.197 | RANDOM | 29.553 |
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 |
2 | 1106 | 1336.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_anti_bump_dis_restr | 0.099 |
s_approx_iso_adps | 0.08 |
s_similar_adp_cmpnt | 0.067 |
s_non_zero_chiral_vol | 0.046 |
s_zero_chiral_vol | 0.045 |
s_angle_d | 0.029 |
s_from_restr_planes | 0.027 |
s_bond_d | 0.009 |
s_rigid_bond_adp_cmpnt | 0.003 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1160 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
SHELXL-97 | refinement |