1P31
Crystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (MurC) from Haemophilus influenzae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | nanovolume | 8.1 | 277 | PEG 4000, glycerol, magnesium chloride, Tris, pH 8.1, nanovolume, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.523 | α = 90 |
b = 92.274 | β = 90 |
c = 118.174 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2002-07-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | 1.0 | ALS | 5.0.3 |
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 | 1.85 | 25 | 90 | 0.064 | 10.8 | 4.45 | 86600 | 77944 | 2 | 2 | 13.3 |
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 | 1.85 | 1.89 | 93 | 0.45 | 3 | 4.5 | 5314 |
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 | SAD | THROUGHOUT | 1.85 | 25 | 73241 | 73241 | 3868 | 89.79 | 0.17135 | 0.17135 | 0.16938 | 0.20836 | RANDOM | 13.859 |
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] | |
2.08 | -1.65 | -0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.523 |
r_scangle_it | 2.96 |
r_scbond_it | 1.879 |
r_angle_refined_deg | 1.112 |
r_mcangle_it | 0.885 |
r_mcbond_it | 0.443 |
r_nbd_refined | 0.194 |
r_symmetry_vdw_refined | 0.177 |
r_symmetry_hbond_refined | 0.164 |
r_xyhbond_nbd_refined | 0.119 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7115 |
Nucleic Acid Atoms | |
Solvent Atoms | 700 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SHELXS | phasing |