2HKA
Crystal structure of bovine NPC2 and cholesterol sulfate complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NEP | PDB ENTRY 1NEP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5 | 295 | PROTEIN SOLUTION: 10-15 MG/ML CHOLESTEROL SULFATE-BOUND NPC2 IN 0.2 M AMMONIUM ACETATE PH 5.0; WELL SOLUTION: 2.0 M AMMONIUM SULFATE, 0.10 M SODIUM ACETATE PH 5.0, 1.0 MM CETYLTRIMETHYLAMMONIUM BROMIDE, EVAPORATION, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 57.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 122.38 | α = 90 |
b = 62.163 | β = 98.62 |
c = 72.449 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | ENRAF-NONIUS | 2005-03-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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) | 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 | 1.81 | 50 | 98.2 | 0.107 | 17.9 | 7.5 | 48283 |
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 | 1.81 | 1.87 | 93 | 0.35 | 4.3 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1NEP | 1.81 | 20 | 48241 | 2431 | 98.2 | 0.195 | 0.214 | RANDOM |
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] | |
-1.347 | -3.644 | 1.42 | -0.073 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 27.1 |
c_angle_deg | 1.38 |
c_improper_angle_d | 1 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3081 |
Nucleic Acid Atoms | |
Solvent Atoms | 371 |
Heterogen Atoms | 157 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
CNS | refinement |