2HB6
Structure of Caenorhabditis elegans leucine aminopeptidase (LAP1)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2EWB |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | 100 MM MES, 2 M AMMONIUM SULFATE, PH 6.00, 5% GLYCEROL, 200 MM SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3 | 58.8 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 131.82 | α = 90 |
b = 131.82 | β = 90 |
c = 125.573 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 63 |
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 | RIGAKU RAXIS IV | MIRRORS | 2006-05-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 50 | 99.9 | 0.058 | 0.093 | 5.7 | 12.4 | 83359 | 83359 |
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 | 2.07 | 99.7 | 0.423 | 0.467 | 1.9 | 11.7 | 8253 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2EWB | 2 | 20 | 80790 | 80783 | 2492 | 99.93 | 0.1523 | 0.14845 | 0.1474 | 0.18279 | RANDOM | 26.818 |
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] | |
-0.15 | -0.07 | -0.15 | 0.22 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.13 |
r_dihedral_angle_4_deg | 19.817 |
r_dihedral_angle_3_deg | 14.67 |
r_scangle_it | 7.393 |
r_dihedral_angle_1_deg | 7.314 |
r_scbond_it | 5.476 |
r_mcangle_it | 3.809 |
r_mcbond_it | 2.866 |
r_angle_refined_deg | 1.248 |
r_nbtor_refined | 0.302 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7330 |
Nucleic Acid Atoms | |
Solvent Atoms | 951 |
Heterogen Atoms | 108 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |