5MCC
Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 1.11 MGy
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 289 | 900mM ammonium sulphate, 100mM monosodium citrate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.52 | 51.16 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 126.972 | α = 90 |
b = 46.64 | β = 108.28 |
c = 172.794 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
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 | PSI PILATUS 6M | 2016-02-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.980 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 164.07 | 99.8 | 0.057 | 0.997 | 12.2 | 3.3 | 65500 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.05 | 99.9 | 0.239 | 0.954 | 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 | pdbid 4XNN | 2 | 164.07 | 62235 | 3220 | 99.7 | 0.1523 | 0.1513 | 0.1728 | RANDOM | 30.18 |
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] | |
-0.35 | -0.4 | 2.45 | -1.5 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.075 |
r_dihedral_angle_4_deg | 22.52 |
r_dihedral_angle_3_deg | 11.423 |
r_dihedral_angle_1_deg | 6.299 |
r_mcangle_it | 2.221 |
r_mcbond_it | 1.702 |
r_mcbond_other | 1.694 |
r_angle_refined_deg | 1.258 |
r_angle_other_deg | 0.888 |
r_chiral_restr | 0.072 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6700 |
Nucleic Acid Atoms | |
Solvent Atoms | 575 |
Heterogen Atoms | 23 |
Software
Software | |
---|---|
Software Name | Purpose |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
DIALS | data reduction |