1GYQ
CRYSTAL STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE FROM LEISHMANIA MEXICANA IN COMPLEX WITH N6-BENZYL-NAD
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1GYP |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 2UL OF SOLUTION CONTAINING 2.25 MG L. MEXICANA GAPDH, 1MM DDT, 1MM EDTA, 1MMPMSF 0.4 MM N6-BENZYL-NAD IN 10MM TRIETHANOLAMINE BUFFER PH 7.0 WAS MIXED WITH 1UL OF RESERVOIR SOLUTION CONTAINING 25 %PEG5000MME, 100MM TRIS PH8.0 AND EQUILIBRATED IN SITTING DROP TRAYS, pH 7.6, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.72 | 54.85 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 97.33 | α = 90 |
b = 125.81 | β = 90 |
c = 137.79 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 1997-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | SSRL | BL7-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.4 | 8 | 84 | 0.138 | 13.8 | 5.9 | 2 | 39118 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||
3.4 | 3.52 | 83 | 0.433 | 43.3 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1GYP | 3.4 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 10864 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 204 |
Software
Software | |
---|---|
Software Name | Purpose |
RAVE | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
RAVE | phasing |