1FDZ
N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REDUCTION
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NAL | ENZYME-3-HYDROXYPYRUVATE COMPLEX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.9 | HANGING DROP VAPOR DIFFUSION. WELL: 53% SATURATED AMMONIUM SULFATE, 75 MILLIMOLAR SODIUM PHOSPHATE BUFFER (PH 6.9). DROP: EQUAL VOLUMES OF WELL AND PRE-REACTED ENZYME, SIALIC ACID AND BOROHYDRIDE MIX (SEE JRNL), vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121 | α = 90 |
b = 121 | β = 90 |
c = 196.12 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | 108 | IMAGE PLATE | RIGAKU RAXIS IIC | MSC MIRROR SYSTEM | 1995-12-09 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | MACSCIENCE M18X |
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 | 2.6 | 15 | 97 | 0.094 | 12.6 | 3.7 | 49914 |
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) | |||||||||||
2.6 | 2.64 | 84.3 | 0.389 | 2.67 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1FDZ (ENZYME-3-HYDROXYPYRUVATE COMPLEX) | 2.6 | 6 | 45800 | 96.8 | 0.2 | 0.2 | 27.3 |
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 |
x_dihedral_angle_d | 23.2 |
x_angle_deg | 1.7 |
x_improper_angle_d | 1.58 |
x_bond_d | 0.012 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9006 |
Nucleic Acid Atoms | |
Solvent Atoms | 228 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |