4MGG
Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PMQ | PDB ENTRY 2PMQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | Protein (17 mb\g/ml, 5mM Mg2+, 20mM Tris buffer (pH=7.9), 5% glycerol); Reservoir (40 % w/v pentaerythritol propoxylate (17/8 PO/OH) 0.2 M magnesium chloride 5.5 0.1 M MES-NaOH (MIDAS F8)); Cryoprotection (Reservoir), pH 6.5, sitting drop, vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.313 | α = 90 |
b = 154.897 | β = 90 |
c = 181.983 | γ = 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 | RAYONIX MX225HE | MIRRORS | 2013-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
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 | 2.2 | 181.983 | 99.9 | 0.184 | 0.184 | 9.3 | 7.3 | 158072 | 158072 | 23.44 |
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 | 2.2 | 2.32 | 99.8 | 0.804 | 0.804 | 0.9 | 7.1 | 22827 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 2PMQ | 2.2 | 40.809 | 157964 | 157964 | 7926 | 99.88 | 0.1536 | 0.1536 | 0.1503 | 0.216 | RANDOM | 29.9691 |
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_dihedral_angle_d | 14.072 |
f_angle_d | 1.384 |
f_chiral_restr | 0.079 |
f_bond_d | 0.014 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21977 |
Nucleic Acid Atoms | |
Solvent Atoms | 1878 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
AMoRE | phasing |