4NGW
Dialyzed HEW lysozyme batch crystallized in 0.5 M YbCl3 and collected at 100 K
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 193L | PDB ENTRY 193L |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.5 | 293 | Dialyzed lysozyme, no buffer added, 0.5 M YbCl3, pH 4.5, Batch crystallization, EVAPORATION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.665 | α = 90 |
b = 78.665 | β = 90 |
c = 37.129 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | PIXEL | DECTRIS PILATUS 6M | MIRRORS | 2013-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.37 | 99.4935 | 99 | 0.051 | 14.1 | 3.4 | 46325 | 15.4 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.37 | 1.45 | 97.4 | 0.294 | 3.48 | 3.1 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 193L | 1.37 | 55.62 | 44465 | 22474 | 2409 | 99.24 | 0.16495 | 0.1625 | 0.18766 | RANDOM | 19.299 |
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 | -0.07 | 0.15 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_sphericity_free | 39.629 |
r_dihedral_angle_2_deg | 35.036 |
r_dihedral_angle_4_deg | 17.658 |
r_dihedral_angle_3_deg | 13.519 |
r_sphericity_bonded | 9.297 |
r_dihedral_angle_1_deg | 5.5 |
r_rigid_bond_restr | 2.219 |
r_scbond_it | 1.956 |
r_mcangle_it | 1.801 |
r_mcbond_it | 1.41 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 5 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHASER | phasing |
CNS | refinement |
XDS | data reduction |
XDS | data scaling |
TRUNCATE | data scaling |
MxCuBE | data collection |