3VAR
Crystal structure of DNPEP, ZnZn form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 281 | 20% 1,4-butanediol, 100 mM MES-NaOH, pH 6.0, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.79 | 55.89 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 245.162 | α = 90 |
b = 245.162 | β = 90 |
c = 245.162 | γ = 90 |
Symmetry | |
---|---|
Space Group | F 4 3 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 | CCD | ADSC QUANTUM 315 | 2011-07-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 1.27582 | APS | 24-ID-C |
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 | 2.25 | 100 | 96 | 0.089 | 12.25 | 30494 | 29272 | -3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.25 | 86.68 | 27811 | 1460 | 95.99 | 0.18996 | 0.18746 | 0.23807 | RANDOM | 24.637 |
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 | 36.612 |
r_dihedral_angle_4_deg | 16.026 |
r_dihedral_angle_3_deg | 14.791 |
r_dihedral_angle_1_deg | 6.792 |
r_angle_refined_deg | 1.68 |
r_angle_other_deg | 0.984 |
r_chiral_restr | 0.101 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3189 |
Nucleic Acid Atoms | |
Solvent Atoms | 173 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data collection |
SHELXD | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |