6TC7 | pdb_00006tc7

PAS-GAF bidomain of Glycine max phytochromeA

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, HANGING DROP	6.5	283.15	0.05 M imidazole, 0.05 M MES, 0.02 M DL-Glutamatic acid monohydrate, 0.02 M DL-Alanine, 0.02M Glycine, 0.02 M DL-Lysine monohydrochloride, 0.02 M DL-Serine, 12% (v/v) Glycerol, 6% (w/v) PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.423	α = 90
b = 113.233	β = 93.521
c = 68.457	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	PSI PILATUS 6M		2019-10-19	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	2.13	44.35	99.5	0.127	0.151	0.08	0.998	10	6.8		46863			36.395

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	2.13	2.19	99.8		1.95	2.306	0.875	0.318	0.9	6.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6TBY	2.13	44.347	46830	1866	99.399	0.191	0.1892	0.2	0.2415	0.25	48.593

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]
0.226		0.067	-0.05		-0.184

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.513
r_dihedral_angle_4_deg	20.255
r_dihedral_angle_3_deg	18.163
r_lrange_it	10.14
r_lrange_other	10.131
r_dihedral_angle_1_deg	8.109
r_scangle_it	7.249
r_scangle_other	7.249
r_mcangle_it	5.693
r_mcangle_other	5.692
r_scbond_it	4.856
r_scbond_other	4.855
r_mcbond_it	3.705
r_mcbond_other	3.704
r_dihedral_angle_other_3_deg	3.479
r_angle_refined_deg	2.469
r_angle_other_deg	1.663
r_chiral_restr_other	1.141
r_nbd_refined	0.234
r_symmetry_nbd_refined	0.215
r_nbd_other	0.2
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.153
r_ncsr_local_group_1	0.136
r_chiral_restr	0.124
r_symmetry_nbtor_other	0.096
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4982
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	100

Software

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