6EK9
Cytosolic copper storage protein Csp from Streptomyces lividans: Cu loaded form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6EIO |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 15 mg/ml protein. 1.4 M ammonium sulfate, 0.1 M MES pH 6.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.6 | 52.74 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 62.081 | α = 90 |
b = 64.138 | β = 90 |
c = 66.003 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 2 2 |
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 | Mirrors | 2016-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.976 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 45.23 | 96.4 | 0.08 | 0.045 | 0.992 | 9.7 | 3.6 | 20701 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.5 | 1.53 | 96.6 | 0.161 | 0.097 | 0.958 | 4.5 | 3.5 |
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 | 6EIO | 1.5 | 45.22 | 19471 | 1228 | 89.35 | 0.2071 | 0.2056 | 0.2308 | RANDOM | 37.874 |
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] | |
-7.89 | 0.64 | 7.25 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.198 |
r_dihedral_angle_4_deg | 21.717 |
r_dihedral_angle_3_deg | 17.075 |
r_sphericity_free | 5.045 |
r_dihedral_angle_1_deg | 4.553 |
r_sphericity_bonded | 4.049 |
r_rigid_bond_restr | 3.947 |
r_angle_refined_deg | 2.056 |
r_angle_other_deg | 1.247 |
r_chiral_restr | 0.127 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 859 |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 20 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Aimless | data reduction |
Coot | model building |
PHASER | phasing |