1OC2
The structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KEP | PDB ENTRY 1KEP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.4 | 30% PEG 4K, 0.1M CITRIC ACID, PH5.4, 0.3M AMMONIUM SULPHATE,, pH 5.40 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.5 | 64.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.41 | α = 90 |
b = 94.829 | β = 90 |
c = 183.543 | 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 | 120 | CCD | ADSC CCD | MIRRORS | 2001-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 1.5 | 91.28 | 98.6 | 0.116 | 4.3 | 3.5 | 179804 |
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 | 1.1 | 1.53 | 98.6 | 0.66 | 1.2 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1KEP | 1.5 | 91.29 | 152105 | 16689 | 98.3 | 0.173 | 0.17 | 0.2 | RANDOM | 15.63 |
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] | |
0.05 | 1.36 | -1.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_chiral_restr | 6.06 |
r_scangle_it | 4.653 |
r_scbond_it | 3.225 |
r_mcangle_it | 2.212 |
r_angle_other_deg | 1.861 |
r_dihedral_angle_1_deg | 1.821 |
r_mcbond_it | 1.565 |
r_symmetry_hbond_refined | 0.648 |
r_symmetry_vdw_other | 0.355 |
r_nbd_other | 0.27 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5479 |
Nucleic Acid Atoms | |
Solvent Atoms | 757 |
Heterogen Atoms | 171 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |