3GQ7
Crystal Structure of the Bacteriophage Phi29 Gene Product 12 N-terminal Fragment
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 10.5 | 298 | 100mM Tris-base at ~pH10.5 and 8% PEG3K, vapor diffusion, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.53 | 65.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.879 | α = 90 |
b = 89.879 | β = 90 |
c = 585.44 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 | MAR CCD 165 mm | 2008-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 1.07 | APS | 14-ID-B |
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 | 2.05 | 50 | 99.8 | 0.077 | 28.259 | 8.3 | 58072 |
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 | 2.05 | 2.12 | 99.6 | 0.315 | 8.4 | 5660 |
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 | 2.05 | 43.81 | 58017 | 2940 | 99.77 | 0.159 | 0.158 | 0.19 | RANDOM | 21.551 |
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] | |
0.59 | 0.3 | 0.59 | -0.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.781 |
r_dihedral_angle_4_deg | 16.812 |
r_dihedral_angle_3_deg | 12.629 |
r_dihedral_angle_1_deg | 6.549 |
r_scangle_it | 2.746 |
r_scbond_it | 1.757 |
r_angle_refined_deg | 1.227 |
r_mcangle_it | 0.96 |
r_mcbond_it | 0.596 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4488 |
Nucleic Acid Atoms | |
Solvent Atoms | 439 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |