6ANZ
Crystal structure of a hypothetical protein from Neisseria gonorrhoeae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | Native protein: Micolytic MCSG1 D8 (1.5 M ammonium sulfate, 100 mM sodium chloride, 100 mM Bis-Tris/HCl, pH 6.5), 25.6 mg/mL NegoA.19190.a.B1.PS38056, cryoprotectant: 25% ethylene glycol, puck MXK4-1, tray 285291d8, I222 crystal form | |
2 | VAPOR DIFFUSION, SITTING DROP | 9 | 289 | Iodide soak for phasing: RigakuReagents JCSG+ C10 (10% PEG20000, 2% dioxane, 100 mM Bicine/NaOH, pH 9.0), 25.6 mg/mL NegoA.19190.a.B1.PS38056, crystal soaked in 20% ethylene glycol and 2.5 M sodium iodide, then flash frozen, puck ZDJ2-5, tray 285290 c10, P212121 crystal form |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.17 | 43 |
2.04 | 40 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 49.93 | α = 90 |
b = 74.4 | β = 90 |
c = 78.56 | 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 | CCD | RAYONIX MX-300 | 2017-06-23 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2017-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.6 | 41.459 | 99.7 | 0.058 | 0.063 | 0.998 | 16.5 | 6.056 | 19646 | -3 | 21.12 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.6 | 1.64 | 98.7 | 0.592 | 0.649 | 0.873 | 2.78 | 5.905 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | FREE R-VALUE | 1.6 | 41.459 | 1.36 | 19645 | 1900 | 99.7 | 0.1842 | 0.1813 | 0.2102 | 0 | 30.8044 |
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 | 13.049 |
f_angle_d | 1.081 |
f_chiral_restr | 0.078 |
f_bond_d | 0.011 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1129 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 10 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XSCALE | data scaling |
PHASER | phasing |
ARP | model building |
Coot | model building |
REFMAC | refinement |
XDS | data reduction |
PDB_EXTRACT | data extraction |