4J89

Different photochemical events of a genetically encoded aryl azide define and modulate GFP fluorescence


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B3P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.528320 mg/mL protein and 100 mM Tris-HCl, 2.4 M (NH4)2SO4, 1+1 microL drop against 85 microL reservoir, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.3748.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.37α = 90
b = 98.11β = 90
c = 102.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2011-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.152.3798.70.0920.09214.67.83131031.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.151000.6420.6421.28.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2B3P2.151.463131031246157598.70.1850.1820.242RANDOM36.21
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]
2.06-1.07-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.08
r_dihedral_angle_3_deg16.617
r_dihedral_angle_4_deg13.962
r_dihedral_angle_1_deg7.811
r_angle_refined_deg1.257
r_angle_other_deg1.167
r_chiral_restr0.033
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.08
r_dihedral_angle_3_deg16.617
r_dihedral_angle_4_deg13.962
r_dihedral_angle_1_deg7.811
r_angle_refined_deg1.257
r_angle_other_deg1.167
r_chiral_restr0.033
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.009
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3615
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms125

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction