3NQU
Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KX5 | TRUNCATED CHAINS A AND B OF PDB ENTRY 1KX5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.9 | 295 | 2 M ammonium sulfate, 0.1 M HEPES (pH 7.9), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 33.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.457 | α = 90 |
b = 61.457 | β = 90 |
c = 185.619 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | 193 | CCD | MARMOSAIC 300 mm CCD | 2009-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.91983 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.5 | 53.22 | 90.88 | 0.154 | 0.121 | 12.15 | 8.5 | 7852 | 7136 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.5 | 2.64 | 90.5 | 0.634 | 0.685 | 2.44 | 6.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | TRUNCATED CHAINS A AND B OF PDB ENTRY 1KX5 | 2.5 | 20 | 7466 | 6806 | 330 | 91.16 | 0.23944 | 0.2363 | 0.23 | 0.3018 | 0.3 | RANDOM | 49.317 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
-2.11 | -1.05 | -2.11 | 3.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.354 |
r_dihedral_angle_4_deg | 26.549 |
r_dihedral_angle_3_deg | 18.185 |
r_dihedral_angle_1_deg | 6.112 |
r_scangle_it | 3.587 |
r_scbond_it | 2.163 |
r_angle_refined_deg | 1.637 |
r_mcangle_it | 1.277 |
r_mcbond_it | 0.678 |
r_chiral_restr | 0.098 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1126 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |