5HGW
Crystal structure of a peptide deformylase from Burkholderia ambifaria
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | Rigaku ReagentsJCSG+ screen E2: 200mM ammonium sulphate, 200mM NaCl, 100mM Na-cacodylate/HCl pH 6.5; BuamA.00078.a.B1.PS02512 at 17.5 mg/ml, tray 267395 e2, puck pud2-3 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.02 | 59.25 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 116.69 | α = 90 |
b = 121.35 | β = 90 |
c = 71.29 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 2 2 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 | CCD | RIGAKU SATURN 944+ | 2015-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.6 | 50 | 99.9 | 0.054 | 0.056 | 29.53 | 11.1 | 66910 | 66817 | -3 | 12.33 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.64 | 99.1 | 0.548 | 0.587 | 4.02 | 7.75 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | PDB entry 4nt8 | 1.6 | 50 | 1.34 | 66804 | 2107 | 99.84 | 0.1544 | 0.1536 | 0.1784 | Random selection | 17.5828 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.438 |
f_angle_d | 1.18 |
f_chiral_restr | 0.08 |
f_bond_d | 0.012 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2738 |
Nucleic Acid Atoms | |
Solvent Atoms | 586 |
Heterogen Atoms | 58 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PHASER | phasing |
PDB_EXTRACT | data extraction |
Coot | model building |