8R45

Phytochromobilin-adducted PAS-GAF bidomain of Glycine max phytochrome A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TC7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2830.04 M Ethylene glycols (0.01M Diethylene glycol; 0.01M Triethylene glycol; 0.01M Tetraethylene glycol; 0.01M Pentaethylene glycol); 0.1 M Tris (base); BICINE pH 9.0; 21% Precipitant Mix (7% v/v MPD; 7% PEG 1000; 7% w/v PEG 3350)
Crystal Properties
Matthews coefficientSolvent content
2.6753.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.542α = 90
b = 112.526β = 92.078
c = 68.37γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2021-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
11.8642.3499.920.99812.886.970335
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)
11.861.9260.592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.8642.3470334357899.9640.170.16930.19231.988
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]
-0.503-0.030.3810.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.205
r_dihedral_angle_6_deg15.96
r_dihedral_angle_2_deg9.705
r_lrange_it8.914
r_lrange_other8.893
r_dihedral_angle_1_deg6.74
r_scangle_it6.464
r_scangle_other6.463
r_mcangle_other4.726
r_mcangle_it4.721
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.205
r_dihedral_angle_6_deg15.96
r_dihedral_angle_2_deg9.705
r_lrange_it8.914
r_lrange_other8.893
r_dihedral_angle_1_deg6.74
r_scangle_it6.464
r_scangle_other6.463
r_mcangle_other4.726
r_mcangle_it4.721
r_scbond_it4.174
r_scbond_other4.173
r_mcbond_it3.156
r_mcbond_other3.147
r_dihedral_angle_other_3_deg1.985
r_angle_refined_deg1.622
r_angle_other_deg1.513
r_symmetry_xyhbond_nbd_refined0.318
r_dihedral_angle_other_2_deg0.271
r_nbd_other0.228
r_nbd_refined0.223
r_symmetry_nbd_other0.188
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.151
r_symmetry_nbd_refined0.108
r_symmetry_nbtor_other0.082
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4979
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing