8R45 | pdb_00008r45

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TC7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		283	0.04 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 coefficient	Solvent content
2.67	53.88

Crystal Data

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

Symmetry
Space Group	P 1 21 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 PILATUS 2M		2021-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.86	42.34	99.92	0.998	12.88	6.9		70335

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.926			0.592

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.86	42.34	70334	3578	99.964	0.17	0.1693	0.1802	0.192	0.1989	31.988

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		-0.03	0.381		0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.205
r_dihedral_angle_6_deg	15.96
r_dihedral_angle_2_deg	9.705
r_lrange_it	8.914
r_lrange_other	8.893
r_dihedral_angle_1_deg	6.74
r_scangle_it	6.464
r_scangle_other	6.463
r_mcangle_other	4.726
r_mcangle_it	4.721
r_scbond_it	4.174
r_scbond_other	4.173
r_mcbond_it	3.156
r_mcbond_other	3.147
r_dihedral_angle_other_3_deg	1.985
r_angle_refined_deg	1.622
r_angle_other_deg	1.513
r_symmetry_xyhbond_nbd_refined	0.318
r_dihedral_angle_other_2_deg	0.271
r_nbd_other	0.228
r_nbd_refined	0.223
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.108
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4979
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	99

Software

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