7D28
Crystal structure of MazF (Form-I) from Deinococcus radiodurans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5CK9 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 20% PEG 5000 MME, 100 mM MES pH 6.5 and 200 mM Ammonium sulfate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.19 | 43.88 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 48.542 | α = 90 |
b = 74.976 | β = 90 |
c = 120.103 | γ = 90 |
Symmetry | |
---|---|
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 | 193 | CCD | ADSC QUANTUM 270 | 2017-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.97933 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.5 | 50 | 100 | 0.078 | 0.081 | 0.021 | 7.2 | 14.4 | 71103 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.5 | 1.53 | 100 | 0.908 | 0.941 | 0.246 | 0.922 | 14.4 |
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 | 5ck9 | 1.5 | 28.82 | 67509 | 3502 | 99.86 | 0.1723 | 0.1709 | 0.2 | RANDOM | 17.64 |
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 |
r_dihedral_angle_2_deg | 28.096 |
r_dihedral_angle_4_deg | 17.844 |
r_dihedral_angle_3_deg | 12.316 |
r_dihedral_angle_1_deg | 7.553 |
r_angle_refined_deg | 1.874 |
r_angle_other_deg | 1.517 |
r_chiral_restr | 0.102 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3308 |
Nucleic Acid Atoms | |
Solvent Atoms | 494 |
Heterogen Atoms | 60 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOLREP | phasing |