3MVX
X-ray structure of the reduced NikA/1 hybrid, NikA/1-Red
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZLQ | PDB ENTRY 1ZLQ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.7 | 293 | 1.8M ammonium sulfate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.09 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86.967 | ¦Á = 90 |
b = 94.616 | ¦Â = 90 |
c = 125.025 | ¦Ã = 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 | CCD | ADSC QUANTUM 315r | Mirrors | 2008-11-28 | M | 0.9796 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.7 | 47.3 | 97 | 0.056 | 22.63 | 7 | 110957 | 25.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.7 | 93 | 0.315 | 5.9 | 6.6 | 16443 |
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 1ZLQ | 1.7 | 47.3 | 107953 | 5682 | 100 | 0.16601 | 0.16401 | 0.20374 | RANDOM | 18.032 |
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] | |
-0.01 | 0.11 | -0.09 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.407 |
r_dihedral_angle_4_deg | 16.129 |
r_dihedral_angle_3_deg | 13.929 |
r_dihedral_angle_1_deg | 6.565 |
r_scangle_it | 5.7 |
r_scbond_it | 3.583 |
r_mcangle_it | 2.331 |
r_angle_refined_deg | 2.256 |
r_mcbond_it | 1.445 |
r_chiral_restr | 0.223 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7892 |
Nucleic Acid Atoms | |
Solvent Atoms | 735 |
Heterogen Atoms | 137 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |