9G8D

Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF192 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G1Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION27930 - 40% MPD, 5 - 15% PEG 8000, 0.1 M MES pH 5.5 - 9.0
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.644α = 90
b = 93.577β = 90
c = 173.945γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97625ESRFID30B

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
12.05945.8399.90.85766.575997
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)
12.0592.110.2011.5

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.05945.8372339371899.820.187760.185920.22409RANDOM33.077
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]
0.561.61-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.789
r_dihedral_angle_4_deg15.012
r_dihedral_angle_3_deg12.877
r_dihedral_angle_1_deg6.129
r_long_range_B_refined5.083
r_long_range_B_other4.981
r_scangle_other3.297
r_mcangle_it2.662
r_mcangle_other2.662
r_scbond_it2.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.789
r_dihedral_angle_4_deg15.012
r_dihedral_angle_3_deg12.877
r_dihedral_angle_1_deg6.129
r_long_range_B_refined5.083
r_long_range_B_other4.981
r_scangle_other3.297
r_mcangle_it2.662
r_mcangle_other2.662
r_scbond_it2.041
r_scbond_other2.041
r_mcbond_it1.696
r_mcbond_other1.695
r_angle_refined_deg1.326
r_angle_other_deg1.306
r_chiral_restr0.055
r_gen_planes_other0.013
r_bond_other_d0.01
r_gen_planes_refined0.008
r_bond_refined_d0.005
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 Atoms7547
Nucleic Acid Atoms
Solvent Atoms656
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing