4ND2
Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (pyruvic acid) and cofactor analog (3-acetylpyridine adenine dinucleotide)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1T2D | PDB ENTRY 1T2D |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | The protein was incubated with 1 mM pyruvate and 100 uM APAD+ for 1 hour on ice prior to crystallization. Reservoir solution was 1.45-1.65 M ammonium sulfate in 0.1 M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.63 | 66.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.83 | α = 90 |
b = 95.83 | β = 90 |
c = 185.64 | 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 | 100 | CCD | MARRESEARCH | 2004-07-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9998 | APS | 19-BM |
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 | 50 | 99.8 | 0.054 | 10.7 | 67287 | 1 |
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 | 2.07 | 97.7 | 0.186 | 8.7 |
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 1T2D | 2 | 49.61 | 60473 | 6816 | 99.8 | 0.19299 | 0.19132 | 0.20788 | RANDOM | 27.258 |
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] | |
0.77 | 0.77 | 0.77 | -2.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.857 |
r_dihedral_angle_4_deg | 12.904 |
r_dihedral_angle_3_deg | 10.662 |
r_dihedral_angle_1_deg | 4.645 |
r_angle_refined_deg | 0.925 |
r_angle_other_deg | 0.664 |
r_chiral_restr | 0.047 |
r_bond_refined_d | 0.004 |
r_gen_planes_refined | 0.002 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4708 |
Nucleic Acid Atoms | |
Solvent Atoms | 415 |
Heterogen Atoms | 118 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |