CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4QRN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.6 | 0.085M AMMONIUM CITRATE, PH 5.6, 0.17M SODIUM ACETATE, 1MM MNCL2, 25% PEG 4000,15% GLYCEROL, VAPOR DIFFUSION,SITTING DROP, TEMPERATURE 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.21 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 60.468 | ¦Á = 90 |
b = 85.486 | ¦Â = 90 |
c = 141.623 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 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 315 | MIRRORS | 2014-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
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 | 1.47 | 50 | 97.7 | 0.102 | 0.102 | 18.2 | 7 | 122409 | -5 |
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) | ||||||||||
1 | 1.47 | 1.5 | 83.1 | 0.79 | 0.79 | 2.1 | 6.4 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MR | THROUGHOUT | 4QRN | 1.47 | 50 | 118586 | 3732 | 98.14 | 0.12151 | 0.12018 | 0.14 | 0.16377 | 0.17 | RANDOM | 21.901 |
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] | |
0.58 | -0.26 | -0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.286 |
r_sphericity_free | 25.107 |
r_dihedral_angle_4_deg | 17.151 |
r_dihedral_angle_3_deg | 12.646 |
r_sphericity_bonded | 10.268 |
r_dihedral_angle_1_deg | 6.242 |
r_scbond_it | 5.703 |
r_scbond_other | 5.703 |
r_scangle_other | 5.513 |
r_rigid_bond_restr | 5.242 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5559 |
Nucleic Acid Atoms | |
Solvent Atoms | 786 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |