2QBY
Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FNN | PDB entry 1FNN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5 | 292 | 25mM HEPES pH 7.5, 50mM sodium chloride, 5% glycerol, 0.5mM TCEP, 15mM spermidine, 15mM sodium cacodylate pH 5.0, 4.4% (w/v) PEG 3350 and 25mM potassium thiocyanate, microbatch, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.81 | 67.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.649 | α = 90 |
b = 199.143 | β = 90 |
c = 213.405 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | ADSC QUANTUM 210 | 2006-04-20 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11111, 0.979578, 0.979733, 0.987379 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.35 | 50 | 98.7 | 25.4 | 6.9 | 24607 | 24287 | 2 | 2 | 119 |
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) | |||||||||||
3.35 | 3.47 | 99 | 0.835 | 1.93 | 5.6 | 2385 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | 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 | MAD | THROUGHOUT | PDB entry 1FNN | 3.35 | 30 | 2 | 2 | 23763 | 22548 | 1215 | 98 | 0.2262 | 0.2262 | 0.2692 | random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_angle_deg | 0.837 |
f_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5881 |
Nucleic Acid Atoms | 1347 |
Solvent Atoms | 4 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MLPHARE | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |