2AT3
1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Imidazole at pH 5.6
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1X8O | PDB entry 1X8O |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 300 | ammonium phosphate, imidazole, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.53 | 19.06 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 70.221 | ¦Á = 90 |
b = 42.743 | ¦Â = 94.09 |
c = 52.886 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 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 | IMAGE PLATE | MAR scanner 345 mm plate | Flat mirror (vertical focusing) | 2002-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.751 | SSRL | BL9-1 |
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 | 19.81 | 97.4 | 0.04 | 0.04 | 20.8 | 3.23 | 81947 | 10 |
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 | 1.04 | 88 | 88.1 | 0.25 | 0.25 | 2.6 | 1.52 | 7330 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R | PDB entry 1X8O | 1 | 19.81 | 81937 | 81937 | 4145 | 97.39 | 0.145 | 0.145 | 0.144 | 0.167 | RANDOM | 8.376 |
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] | |
0.13 | -0.16 | 0.13 | -0.28 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.95 |
r_dihedral_angle_3_deg | 13.355 |
r_dihedral_angle_4_deg | 7.792 |
r_dihedral_angle_1_deg | 7.381 |
r_sphericity_free | 7.035 |
r_sphericity_bonded | 3.532 |
r_scangle_it | 3.187 |
r_scbond_it | 2.584 |
r_mcangle_it | 1.896 |
r_angle_refined_deg | 1.658 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1798 |
Nucleic Acid Atoms | |
Solvent Atoms | 276 |
Heterogen Atoms | 48 |
Software
Software | |
---|---|
Software Name | Purpose |
d*TREK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
CrystalClear | data scaling |