2X0A
MPD-Lysozyme structure at 55.5 keV using a TRIXXEL CsI-aSi based digital imager and the new ESRF U22 undulator source at ID15
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2CGI | PDB ENTRY 2CGI |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | HANGING DROP METHOD AT 295K. DROP IS 1 MICROL OF 50 MG/ML PROTEIN AND 1 MICROL OF WELL SOLUTION. WELL VOLUME IS 1ML OF 70 % MPD FROM HAMPTON RESEARCH. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.01 | 39 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 77.207 | α = 90 |
b = 77.207 | β = 90 |
c = 37.767 | 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 | FLAT PANEL | TRIXXEL | SINGLE BOUNCE BENT BRAGG MONO | 2008-07-19 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | CCD | ADSC CCD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID15B | 0.22 | ESRF | ID15B |
2 | SYNCHROTRON | NSLS BEAMLINE X6A | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.52 | 20 | 99.2 | 0.06 | 19.6 | 6.6 | 17977 | 2 | 11.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.52 | 1.54 | 89.1 | 0.24 | 3.4 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 2CGI | 1.52 | 19.3 | 17023 | 915 | 100 | 0.14874 | 0.14621 | 0.19902 | RANDOM | 13.263 |
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] | |
-0.45 | -0.45 | 0.9 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.762 |
r_dihedral_angle_4_deg | 18.328 |
r_dihedral_angle_3_deg | 12.638 |
r_sphericity_free | 5.889 |
r_dihedral_angle_1_deg | 5.638 |
r_scangle_it | 3.856 |
r_sphericity_bonded | 3.264 |
r_scbond_it | 2.666 |
r_mcangle_it | 1.841 |
r_rigid_bond_restr | 1.49 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1000 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms | 12 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |