2PE5
Crystal Structure of the Lac Repressor bound to ONPG in repressed state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1EFA | PDB entry 1EFA |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 281 | 1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
5.03 | 75.52 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 253.08 | α = 90 |
b = 253.08 | β = 90 |
c = 203.247 | γ = 120 |
Symmetry | |
---|---|
Space Group | H 3 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 | IMAGE PLATE | MAR scanner 300 mm plate | Osmic mirrors | 2006-03-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 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 | 3.5 | 20 | 99.89 | 0.176 | 0.176 | 7.3 | 9.1 | 31342 | 29717 | -3 | -3 | 25.4 |
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) | ||||||||||
3.5 | 3.6 | 99.7 | 0.504 | 0.504 | 4.37 | 6.9 | 2090 |
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 | PDB entry 1EFA | 3.5 | 19.98 | 29717 | 29717 | 1581 | 99.86 | 0.23616 | 0.23616 | 0.23347 | 0.28656 | RANDOM | 53.844 |
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] | |
-0.02 | -0.01 | -0.02 | 0.04 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.867 |
r_dihedral_angle_3_deg | 20.917 |
r_dihedral_angle_4_deg | 17.201 |
r_dihedral_angle_1_deg | 5.896 |
r_scangle_it | 1.752 |
r_angle_refined_deg | 1.627 |
r_mcangle_it | 0.983 |
r_scbond_it | 0.927 |
r_mcbond_it | 0.551 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7418 |
Nucleic Acid Atoms | 1046 |
Solvent Atoms | |
Heterogen Atoms | 63 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |