4RSE
Crystal structure of RPE65 in complex with MB-001 and palmitate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FSN |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 281 | 40% PEG 300 200 mM NaCl 100 mM CHES-NAOH, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.16 | 61.13 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 175.639 | ¦Á = 90 |
b = 175.639 | ¦Â = 90 |
c = 86.611 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 65 |
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 | ADSC QUANTUM 315r | 2014-08-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.0750 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.39 | 50 | 99.15 | 59881 | 59880 | -3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 3FSN | 2.39 | 47.9 | 59880 | 56801 | 3079 | 99.15 | 0.19784 | 0.19576 | 0.2357 | RANDOM | 47.059 |
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] | |
0.54 | 0.27 | 0.54 | -1.75 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.122 |
r_sphericity_bonded | 18.333 |
r_dihedral_angle_4_deg | 17.243 |
r_dihedral_angle_3_deg | 13.885 |
r_dihedral_angle_1_deg | 6.939 |
r_long_range_B_refined | 6.6 |
r_long_range_B_other | 6.558 |
r_scangle_other | 4.197 |
r_mcangle_it | 3.975 |
r_mcangle_other | 3.975 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8250 |
Nucleic Acid Atoms | |
Solvent Atoms | 401 |
Heterogen Atoms | 82 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
REFMAC | refinement |
XDS | data reduction |
REFMAC | phasing |