8RJT | pdb_00008rjt

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I6 intermediate state.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G1Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2791.0 - 2.2 M ammonium sulphate, 2 - 12% PEG 1000, 0.1 M HEPES pH 6.8 - 7.7, 0.025% low-melt agarose
Crystal Properties
Matthews coefficientSolvent content
3.9769.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.204α = 90
b = 185.204β = 90
c = 182.012γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX170-HS2018-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.30040SLAC LCLSMFX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.4925.4499.90.88226.4177.164685
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.560.012

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.4925.4457774184092.160.210190.208940.2130.249820.2485RANDOM70.57
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]
-0.39-0.2-0.391.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.391
r_dihedral_angle_4_deg15.522
r_dihedral_angle_3_deg13.926
r_long_range_B_refined7.907
r_long_range_B_other7.894
r_dihedral_angle_1_deg5.782
r_scangle_other4.695
r_mcangle_it4.323
r_mcangle_other4.323
r_scbond_it2.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.391
r_dihedral_angle_4_deg15.522
r_dihedral_angle_3_deg13.926
r_long_range_B_refined7.907
r_long_range_B_other7.894
r_dihedral_angle_1_deg5.782
r_scangle_other4.695
r_mcangle_it4.323
r_mcangle_other4.323
r_scbond_it2.745
r_scbond_other2.745
r_mcbond_other2.615
r_mcbond_it2.614
r_angle_refined_deg1.235
r_angle_other_deg1.2
r_chiral_restr0.041
r_gen_planes_other0.007
r_bond_other_d0.005
r_gen_planes_refined0.004
r_bond_refined_d0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7351
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata scaling
DIALSdata reduction
PRIMEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building