4CKC
Vaccinia virus capping enzyme complexed with SAH (monoclinic form)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VDW | PDB ENTRY 2VDW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | PROTEIN SOLUTION AT 4 MG/ML IN 40 MM TRIS-HCL, PH 8.0, 200 MM NACL, 5 MM DTT WITH 5 MM ADOMET. RESERVOIR SOLUTION: 0.1 M TRIS-HCL, PH 7.5, 0.2 M LICL, 0.2M (NH4)2SO4, 15% PEG4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.71 | α = 90 |
b = 200.26 | β = 102.18 |
c = 128.1 | 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 | 100 | CCD | MARRESEARCH | 2004-11-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
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 | 2.9 | 50 | 92 | 0.14 | 5.05 | 1.88 | 62825 |
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 | 2.9 | 2.97 | 81.1 | 0.4 | 2.13 | 1.83 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2VDW | 2.9 | 125 | 59652 | 3174 | 93.55 | 0.25697 | 0.25485 | 0.29706 | RANDOM | 42.427 |
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] | |
-1.57 | 0.52 | -3.01 | 3.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.478 |
r_dihedral_angle_4_deg | 16.253 |
r_dihedral_angle_3_deg | 16.218 |
r_dihedral_angle_1_deg | 6.341 |
r_long_range_B_refined | 2.468 |
r_long_range_B_other | 2.468 |
r_mcangle_it | 1.469 |
r_mcangle_other | 1.469 |
r_angle_refined_deg | 1.01 |
r_scangle_other | 0.809 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17909 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |