9FEK
Crystal structure of guanidinase from Nitrospira inopinata
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 295.15 | 0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4 |
2 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 295.15 | 0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4 |
3 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 295.15 | 0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.35 | 47.55 |
2.35 | 47.55 |
2.35 | 47.55 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 98.965 | α = 90 |
b = 164.791 | β = 90.03 |
c = 143.965 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
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 | Vertical CRL / Horizontal Eliptical mirror | 2022-06-04 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Vertical CRL / Horizontal Eliptical mirror | 2023-12-05 | M | SINGLE WAVELENGTH | |||||
3 | 3 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Vertical CRL / Horizontal Eliptical mirror | 2023-12-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.9184 | ESRF | ID30B |
2 | SYNCHROTRON | ESRF BEAMLINE ID30B | 1.48253 | ESRF | ID30B |
3 | SYNCHROTRON | ESRF BEAMLINE ID30B | 1.89289 | ESRF | ID30B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.58 | 45.01 | 92.89 | 0.1064 | 0.1318 | 0.07673 | 0.991 | 4.66 | 2.3 | 583936 | 22.07 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.58 | 1.636 | 85.24 | 1.191 | 1.506 | 0.9081 | 0.256 | 0.56 | 2.1 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.58 | 45.01 | 1.33 | 583176 | 2001 | 92.9 | 0.1999 | 0.1998 | 0.2142 |
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 | 14.52 |
f_angle_d | 1.092 |
f_chiral_restr | 0.065 |
f_plane_restr | 0.013 |
f_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 34269 |
Nucleic Acid Atoms | |
Solvent Atoms | 2815 |
Heterogen Atoms | 144 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
XSCALE | data scaling |
XDS | data reduction |
PHASER | phasing |