2I02
CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like family protein (NPUN_R6570) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.5 | 277 | 0.2M NaCl, 40.0% PEG-300, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.38 | 47.9 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 103.646 | α = 90 |
b = 103.646 | β = 90 |
c = 109.695 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 63 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 | ADSC QUANTUM 315 | Flat mirror (vertical focusing) | 2006-07-02 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.979197,0.918370 | SSRL | BL11-1 |
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 | 1.8 | 29.921 | 100 | 0.117 | 0.117 | 4.8 | 10.3 | 32823 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.8 | 1.85 | 100 | 0.946 | 0.946 | 0.8 | 10.6 | 2377 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.8 | 29.921 | 32793 | 1663 | 99.99 | 0.178 | 0.177 | 0.204 | RANDOM | 25.749 |
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] | |
-0.55 | -0.27 | -0.55 | 0.82 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.584 |
r_dihedral_angle_4_deg | 13.334 |
r_dihedral_angle_3_deg | 13.209 |
r_scangle_it | 7.245 |
r_dihedral_angle_1_deg | 6.242 |
r_scbond_it | 5.215 |
r_mcangle_it | 3.393 |
r_mcbond_it | 2.36 |
r_angle_refined_deg | 1.496 |
r_angle_other_deg | 0.88 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2262 |
Nucleic Acid Atoms | |
Solvent Atoms | 175 |
Heterogen Atoms | 53 |
Software
Software | |
---|---|
Software Name | Purpose |
MolProbity | model building |
SHELX | phasing |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
SHELXD | phasing |
SHARP | phasing |