2XB4
Crystal structures of zinc containing Adenylate kinase from Desulfovibrio gigas
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 0.2 M TARTRATE NA/K, 0.1 M MES (PH 6.5) AND 20% PEG 2K OR 8K (THE PROTEIN:WELL SOLUTION RATIO IN THE DROP WAS 1:1, 1:2 OR 1:3 WITH THE FINAL DROP VOLUME OF 4, 6 OR 8 MICRO LITRE) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.59 | 65.5 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 39.39 | ¦Á = 90 |
b = 119.44 | ¦Â = 90 |
c = 149.59 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 2 2 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 | 110 | CCD | ADSC QUANTUM 4 | M | MAD |
Radiation Source | |||||
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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 | 1.8 | 23.19 | 99.5 | 0.07 | 10.2 | 6 | 31474 | 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 | 1.8 | 1.85 | 95.5 | 0.34 | 1.6 | 6 |
Refinement
Statistics | |||||||||||||||||||
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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 | MAD | THROUGHOUT | NONE | 1.8 | 23.92 | 31474 | 1671 | 99.53 | 0.17967 | 0.17793 | 0.21152 | RANDOM | 14.049 |
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] | |
0.13 | -0.08 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.751 |
r_dihedral_angle_4_deg | 22.409 |
r_dihedral_angle_3_deg | 16.215 |
r_scangle_it | 6.289 |
r_dihedral_angle_1_deg | 5.814 |
r_scbond_it | 3.865 |
r_angle_refined_deg | 2.214 |
r_mcangle_it | 2.081 |
r_mcbond_it | 1.276 |
r_chiral_restr | 0.207 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1718 |
Nucleic Acid Atoms | |
Solvent Atoms | 320 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
autoSHARP | phasing |