1U9A
HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AAK | PDB ENTRY 1AAK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | PROTEIN WAS CRYSTALLIZED IN THE SPACE GROUP P21 FROM 9% PEG 4000, 9% ISOPROPANOL, 0.1 M HEPES, PH 7.5 SYMMETRY OPERATIONS FOR NON-STANDARD SETTING: P 21: X, Y,Z -X,Y+1/2,-Z |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.04 | α = 90 |
b = 35.18 | β = 111.2 |
c = 58.1 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 281 | IMAGE PLATE | MARRESEARCH | 1996-05-26 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
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 | 20 | 91 | 0.12 | 0.12 | 8.9 | 3 | 12295 | 1 | 25.1 |
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 | 2.03 | 94 | 0.42 | 0.42 | 3.8 | 6.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1AAK | 2 | 10 | 11707 | 11707 | 587 | 84 | 0.16 | 0.25 | RANDOM |
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 | |
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Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 15.229 |
t_it | 2.435 |
t_angle_deg | 1.289 |
t_nbd | 0.068 |
t_bond_d | 0.012 |
t_gen_planes | 0.011 |
t_trig_c_planes | 0.007 |
t_incorr_chiral_ct | |
t_pseud_angle |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1283 |
Nucleic Acid Atoms | |
Solvent Atoms | 103 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
TNT | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |