6TC5

Phytochromobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TBY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	283.15	100 mM Tris/HCl pH 8.5, 500 mM NaCl, 9% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.875	α = 90
b = 133.875	β = 90
c = 46.951	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2017-09-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.1	43.82	99.1	0.151	0.175	0.088	0.997	10.7	7.4		28169			38.875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	98.5		1.62	1.873	0.933	0.536	1.3	7.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6TBY	2.1	43.82	28161	1401	98.974	0.199	0.197	0.2295	38.875

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]
-0.003	-0.001		-0.003		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.166
r_dihedral_angle_4_deg	20.044
r_dihedral_angle_3_deg	16.557
r_dihedral_angle_other_3_deg	13.943
r_lrange_it	8.538
r_lrange_other	8.492
r_dihedral_angle_1_deg	7.532
r_scangle_it	6.262
r_scangle_other	6.26
r_mcangle_it	5.092
r_mcangle_other	5.091
r_scbond_it	4.043
r_scbond_other	4.042
r_mcbond_other	3.454
r_mcbond_it	3.453
r_angle_refined_deg	1.87
r_angle_other_deg	1.382
r_chiral_restr_other	1.011
r_symmetry_xyhbond_nbd_other	0.231
r_symmetry_xyhbond_nbd_refined	0.231
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.184
r_nbd_other	0.183
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.161
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2424
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing