1VL6
Crystal structure of NAD-dependent malic enzyme (TM0542) from Thermotoga maritima at 2.61 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K | |
2 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.85 | 56.87 |
3.12 | 60.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 143.963 | α = 90 |
b = 143.963 | β = 90 |
c = 163.428 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC | 2003-07-25 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | M | MAD | |||||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 | |
2 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.019943, 0.979762, 0.979619 | ALS | 8.3.1 |
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 | ||||||||
1,2 | 2.6 | 47.12 | 98.84 | 0.054 | 16.77 | 3.26 | 57871 | 74.19 |
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 | 2.6 | 2.69 | 96.26 | 0.551 | 1.84 | 2.86 | 5591 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.61 | 47.12 | 55267 | 2333 | 98.53 | 0.1938 | 0.19189 | 0.23929 | RANDOM | 61.902 |
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] | |
1.1 | 0.55 | 1.1 | -1.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.556 |
r_dihedral_angle_3_deg | 17.945 |
r_dihedral_angle_4_deg | 17.668 |
r_scangle_it | 8.133 |
r_dihedral_angle_1_deg | 6.65 |
r_scbond_it | 5.8 |
r_mcangle_it | 2.64 |
r_angle_refined_deg | 1.658 |
r_mcbond_it | 1.521 |
r_angle_other_deg | 0.933 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 11096 |
Nucleic Acid Atoms | |
Solvent Atoms | 44 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
MOSFLM | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
SHARP | phasing |
REFMAC | refinement |