1REM
HUMAN LYSOZYME WITH MAN-B1,4-GLCNAC COVALENTLY ATTACHED TO ASP53
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1REY | PDB ENTRY 1REY EXCEPT RESIDUE NAG 131 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 4.5 | 5M AMMONIUM NITRATE IN 20MM SODIUM ACETATE (PH 4.5) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.18 | 43.5 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 36.39 | α = 90 |
b = 116.38 | β = 90 |
c = 30.91 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | IMAGE PLATE | RIGAKU RAXIS IIC | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.07 | 36.4 | 94.9 | 0.057 | 3.05 | 7438 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1REY EXCEPT RESIDUE NAG 131 | 2.1 | 8 | 3 | 7060 | 0.168 | 0.168 | 0.248 | 21.07 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 24.22 |
x_angle_deg | 1.637 |
x_improper_angle_d | 1.428 |
x_bond_d | 0.011 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1029 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 34 |
Software
Software | |
---|---|
Software Name | Purpose |
R-AXIS | data collection |
R-AXIS | data reduction |
X-PLOR | model building |
X-PLOR | refinement |
R-AXIS | data scaling |
X-PLOR | phasing |