6G20

Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its functional Meta-F intermediate state.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION279(NH4)2SO4, VAPOR DIFFUSION, TEMPERATURE 279K
Crystal Properties
Matthews coefficientSolvent content
4.0369.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.114α = 90
b = 183.114β = 90
c = 179.655γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9724ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.1647.791000.0310.99918.32095000
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.162.281000.4090.6721.920

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT6G1Z2.16158.5890118484299.980.21020.209050.23225RANDOM50.886
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]
2.011.012.01-6.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.457
r_dihedral_angle_4_deg15.968
r_dihedral_angle_3_deg12.358
r_long_range_B_refined6.961
r_long_range_B_other6.961
r_dihedral_angle_1_deg5.489
r_scangle_other3.023
r_mcangle_it2.427
r_mcangle_other2.426
r_scbond_it1.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.457
r_dihedral_angle_4_deg15.968
r_dihedral_angle_3_deg12.358
r_long_range_B_refined6.961
r_long_range_B_other6.961
r_dihedral_angle_1_deg5.489
r_scangle_other3.023
r_mcangle_it2.427
r_mcangle_other2.426
r_scbond_it1.862
r_scbond_other1.862
r_angle_refined_deg1.468
r_mcbond_it1.423
r_mcbond_other1.42
r_angle_other_deg0.835
r_chiral_restr0.071
r_bond_other_d0.015
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.004
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 Atoms7512
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms262

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing