3WCK | pdb_00003wck

Crystal structure of monomeric photosensitizing fluorescent protein, Supernova


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A8S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22930.1M SODIUM ACETATE, 2.2M SODIUM CHLORIDE, 0.2M LITHIUM SULFATE, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.252α = 70.57
b = 89.304β = 89.95
c = 109.885γ = 71.62
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12APhoton FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35097.90.0723.53.188149-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3497.10.3235.13.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3A8S2.32083631443297.50.1840.1810.190.2340.23RANDOM28.1
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]
0.31-0.860.550.52-0.74-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.286
r_dihedral_angle_4_deg18.214
r_dihedral_angle_3_deg16.921
r_dihedral_angle_1_deg7.025
r_angle_refined_deg1.942
r_angle_other_deg0.856
r_chiral_restr0.103
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13795
Nucleic Acid Atoms
Solvent Atoms508
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling