3ZYM
Structure of CALM (PICALM) in complex with VAMP8
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HF8 | PDB ENTRY 1HF8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 289 | CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING EQUAL AMOUNTS (200-400 NL) OF PROTEIN (15 MG/ML IN 20 MM HEPES PH 7.4, 120 MM NACL, 4 MM DTT) AND RESERVOIR SOLUTION (100 MM PHOSPHATE-CITRATE PH 4.2, 200 MM NACL, 50% (V/V) PEG-200) AND EQUILIBRATED AGAINST 80 UL OF RESERVOIR SOLUTION AT 16C. CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION (5-60 S) IN RESERVOIR SOLUTION SUPPLEMENTED WITH 25% GLYCEROL AND WERE RAPIDLY CRYOCOOLED IN LIQUID N2 OR A 100 K STREAM OF N2 GAS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.49 | 64.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 161.051 | α = 90 |
b = 100.26 | β = 118.88 |
c = 104.021 | 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 | ADSC CCD | MIRRORS | 2010-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 |
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 | 91.1 | 99.7 | 0.08 | 10 | 3.7 | 93133 | -3 | 33.81 |
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 | 2.03 | 2.08 | 99.8 | 0.73 | 1.9 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 1HF8 | 2.03 | 45.573 | 1.34 | 93104 | 4667 | 99.6 | 0.1815 | 0.1807 | 0.198 | 42.38 |
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] | |
1.0877 | 2.8613 | -3.7334 | 2.6457 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.982 |
f_angle_d | 0.913 |
f_chiral_restr | 0.063 |
f_bond_d | 0.008 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6713 |
Nucleic Acid Atoms | |
Solvent Atoms | 473 |
Heterogen Atoms | 71 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |