8RJU | pdb_00008rju

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I7 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
3.8568.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.9α = 90
b = 182.9β = 90
c = 180.841γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX170-HS2018-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.31196SLAC 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
12.845.771000.92817.6890.544427
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)
12.82.870.205

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 REPLACEMENTTHROUGHOUT2.845.7741468195997.750.277950.275920.27290.319560.3164RANDOM55.688
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.16
r_dihedral_angle_4_deg16.813
r_dihedral_angle_3_deg14.856
r_long_range_B_refined8.034
r_long_range_B_other8.033
r_dihedral_angle_1_deg5.91
r_mcangle_it3.79
r_mcangle_other3.79
r_scangle_other3.58
r_mcbond_it2.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.16
r_dihedral_angle_4_deg16.813
r_dihedral_angle_3_deg14.856
r_long_range_B_refined8.034
r_long_range_B_other8.033
r_dihedral_angle_1_deg5.91
r_mcangle_it3.79
r_mcangle_other3.79
r_scangle_other3.58
r_mcbond_it2.251
r_mcbond_other2.251
r_scbond_it2.067
r_scbond_other2.067
r_angle_refined_deg1.262
r_angle_other_deg1.166
r_chiral_restr0.043
r_gen_planes_other0.009
r_gen_planes_refined0.005
r_bond_refined_d0.003
r_bond_other_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 Atoms7347
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms157

Software

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