5AFP
Neuronal calcium sensor-1 (NCS-1)from Rattus norvegicus complex with rhodopsin kinase peptide from Homo sapiens
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2YOU | PDB ENTRY 2YOU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.12M ALCOHOLS (1,6-HEXANEDIOL; 1- BUTANOL;1,PROPANEDIOL(RACEMIC); 2-PROPONOL; 1, 4-BUTANEDIOL; 1,3- PROPANEDIOL); 0.1M BUFFER 2 (SODIUM HEPES; MOPS ACID PH 7.5); P550MME_P20K 30%. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.69 | α = 90 |
b = 93.69 | β = 92.25 |
c = 55.71 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2014-07-12 | 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 | 2.3 | 48 | 99.2 | 0.04 | 15.8 | 3.3 | 18488 | 2 |
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 | 2.3 | 2.36 | 94.3 | 0.37 | 2.2 | 2.6 |
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 2YOU | 2.3 | 47.86 | 17512 | 956 | 99.16 | 0.22708 | 0.22556 | 0.25515 | RANDOM | 46.458 |
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] | |
0.74 | -0.34 | -0.36 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.02 |
r_dihedral_angle_4_deg | 14.574 |
r_dihedral_angle_3_deg | 14.328 |
r_dihedral_angle_1_deg | 4.913 |
r_mcangle_it | 2.452 |
r_scbond_it | 2.387 |
r_mcbond_it | 1.689 |
r_mcbond_other | 1.682 |
r_angle_refined_deg | 1.238 |
r_angle_other_deg | 0.738 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2988 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |