2W00
Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 1 UL OF PROTEIN IN 20 MM PHOSPHATE PH 7.5, 100 MM KCL, 5 MM ATP WAS MIXED WITH 2 UL OF RESERVOIR, CONTAINING 0.2 M LI2SO4, 8 % PEG 20K, 8 % PEG 550 MME, 1.5 MM DTT, 277 K, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.91 | α = 90 |
b = 129.922 | β = 90 |
c = 161.01 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | MIRRORS | 2006-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X12 | EMBL/DESY, HAMBURG | X12 |
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 | 2.6 | 20 | 100 | 0.13 | 17.9 | 9.4 | 80316 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.6 | 2.64 | 100 | 0.5 | 5.8 | 9.1 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | NONE | 2.6 | 19.97 | 79250 | 977 | 100 | 0.221 | 0.221 | 0.265 | RANDOM | 40.95 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.04 | 0.01 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.133 |
r_dihedral_angle_4_deg | 26.097 |
r_dihedral_angle_3_deg | 21.712 |
r_dihedral_angle_1_deg | 21.286 |
r_scangle_it | 5.286 |
r_scbond_it | 3.625 |
r_mcangle_it | 2.036 |
r_angle_refined_deg | 1.418 |
r_mcbond_it | 1.391 |
r_nbtor_refined | 0.335 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13740 |
Nucleic Acid Atoms | |
Solvent Atoms | 582 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Auto-Rickshaw | phasing |