4XG1
Psychromonas ingrahamii diaminopimelate decarboxylase with LLP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 281 | 28%(W/V) PEG 3350, 100mM BIS-TRIS PROPANE (PH 6.0), 200mM POTASSIUM THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.21 | 44.3 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 89.96 | α = 90 |
b = 103.13 | β = 94.77 |
c = 93.59 | 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 | CCD | ADSC QUANTUM 315r | 2014-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.954 | Australian Synchrotron | MX2 |
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 | 2.5 | 69.17 | 99.8 | 0.072 | 0.077 | 20.3 | 7.3 | 58922 |
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 | 2.5 | 2.64 | 99.9 | 0.146 | 0.157 | 11.6 | 7.5 |
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 | PDB ID 3N2B | 2.5 | 19.85 | 57729 | 1014 | 99.49 | 0.2119 | 0.2113 | 0.24589 | RANDOM | 31.382 |
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] | |
0.07 | 0.09 | -0.03 | -0.06 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.689 |
r_dihedral_angle_4_deg | 18.905 |
r_dihedral_angle_3_deg | 15.737 |
r_long_range_B_refined | 6.887 |
r_long_range_B_other | 6.886 |
r_dihedral_angle_1_deg | 6.591 |
r_scangle_other | 4.399 |
r_mcangle_it | 4.294 |
r_mcangle_other | 4.294 |
r_mcbond_it | 2.688 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 12467 |
Nucleic Acid Atoms | |
Solvent Atoms | 391 |
Heterogen Atoms | 148 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |
REFMAC | refinement |
Coot | model building |
XDS | data reduction |
Auto-Rickshaw | phasing |