4YWO
Mercuric reductase from Metallosphaera sedula
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1ZK7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 300 | 0.085 M TRIS, 15% v/v glycerol, 14% w/v PEG400, 0.19 M LiSO4, and 20 mg/mL protein |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.68 | 55.85 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 55.679 | α = 90 |
b = 95.895 | β = 90 |
c = 104.484 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 2 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2014-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9537 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.62 | 70.65 | 99.1 | 0.1687 | 0.1957 | 13.2 | 5.9 | 71541 |
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 | 1.62 | 1.64 | 85.7 | 0.468 | 2.1 | 3.6 |
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 | 1ZK7 | 1.62 | 70.65 | 67801 | 3604 | 98.83 | 0.16975 | 0.1683 | 0.197 | RANDOM | 24.543 |
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] | |
0.02 | -0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.389 |
r_dihedral_angle_4_deg | 17.826 |
r_dihedral_angle_3_deg | 12.202 |
r_long_range_B_refined | 7.251 |
r_long_range_B_other | 7.214 |
r_scangle_other | 6.277 |
r_dihedral_angle_1_deg | 5.907 |
r_scbond_it | 4.23 |
r_scbond_other | 4.225 |
r_mcangle_it | 3.162 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3367 |
Nucleic Acid Atoms | |
Solvent Atoms | 212 |
Heterogen Atoms | 83 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
HKL-2000 | data reduction |
XDS | data scaling |
HKL-2000 | data scaling |
Aimless | data scaling |
MOLREP | phasing |
Coot | model building |