8RJP | pdb_00008rjp

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I2 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
3.9568.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.735α = 90
b = 184.735β = 90
c = 181.699γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX170-HSCompound refractive lenses2018-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.30087SLAC 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
12.4325.6499.90.90125.8220.469042
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)
12.432.490.027

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 REPLACEMENTTHROUGHOUT2.4325.6465936197798.360.203230.202290.20580.233690.2364RANDOM63.366
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]
-0.46-0.23-0.461.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.375
r_dihedral_angle_4_deg14.646
r_dihedral_angle_3_deg13.412
r_long_range_B_refined6.31
r_long_range_B_other6.31
r_dihedral_angle_1_deg5.592
r_scangle_other3.928
r_mcangle_it3.648
r_mcangle_other3.648
r_scbond_it2.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.375
r_dihedral_angle_4_deg14.646
r_dihedral_angle_3_deg13.412
r_long_range_B_refined6.31
r_long_range_B_other6.31
r_dihedral_angle_1_deg5.592
r_scangle_other3.928
r_mcangle_it3.648
r_mcangle_other3.648
r_scbond_it2.261
r_scbond_other2.261
r_mcbond_it2.156
r_mcbond_other2.154
r_angle_refined_deg1.265
r_angle_other_deg1.15
r_chiral_restr0.04
r_gen_planes_other0.017
r_gen_planes_refined0.007
r_bond_other_d0.004
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 Atoms7492
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms141

Software

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