6TZ8
Crystal structure of Cryptococcus neoformans Calceineurin A, Calcineurin B, and FKBP12 with FK-506
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1TCO |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | CRYPTOCOCCUS NEOFORMANS CALCINEURIN A (CRNEC.00174.A.EX14), CALCINEURIN B (CRNEC.01011.A.FX11), AND FKBP12 (CRNEC.18272.A.DB13) WITH FK-506 IN 25MM MES PH6.4, 150MM NACL, 0.5MM TCEP, 5MM CACL2, 5UM FK506 WAS CRYSTALLIZED AT 9.38MG/ML AGAINST MORPHEUS II CONDITION A3 CONTAINING 30MM LITHIUM SULFATE, 30MM SODIUM SULFATE, 30MM POTASSIUM SULFATE, 0.1M MOPSO/0.1M BIS-TRIS PH6.5, 10% W/V PEG8000 AND 20% W/V 1, 5 PENTANEDIOL. CRYSTALS WERE DIRECTLY CRYO-PROTECTED IN 20% ETHYLENE GLYCOL |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.24 | 62 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 118.72 | α = 90 |
b = 120.7 | β = 90 |
c = 134.96 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | BERYLLIUM LENSES | 2016-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.9787 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 3.3 | 50 | 99.9 | 0.196 | 0.215 | 0.992 | 8.62 | 6.2 | 29795 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.3 | 3.39 | 99.9 | 0.587 | 0.642 | 0.918 | 3.3 | 6.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation 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 | FREE R-VALUE | 1TCO | 3.3 | 44.57 | 1.34 | 29717 | 1479 | 99.65 | 0.2013 | 0.1992 | 0.2434 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.854 |
f_angle_d | 0.651 |
f_chiral_restr | 0.042 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 10119 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms | 141 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PHASER | phasing |