8R49

Plastidial phosphorylase Pho1 from Solanum tuberosum in complex with beta cyclodextrin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8R48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.1 M Tris-HCl, 20 % PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 218.63	α = 90
b = 136.728	β = 91.47
c = 123.155	γ = 90

Symmetry
Space Group	C 1 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 PILATUS 6M		2023-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976256	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	123.114	98	0.09	0.995	7.4	3		87204

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85			0.818	0.654

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	123.114	87192	4411	97.836	0.219	0.2176	0.239	RANDOM	88.194

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]
-2.278		1.78	6.759		-4.566

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.186
r_dihedral_angle_6_deg	13.361
r_lrange_it	7.763
r_lrange_other	7.763
r_dihedral_angle_1_deg	6.518
r_dihedral_angle_2_deg	5.871
r_mcangle_it	3.858
r_mcangle_other	3.858
r_scangle_it	3.662
r_scangle_other	3.662
r_mcbond_it	2.324
r_mcbond_other	2.324
r_scbond_it	2.098
r_scbond_other	2.098
r_angle_refined_deg	1.077
r_angle_other_deg	0.402
r_nbd_refined	0.222
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.18
r_nbd_other	0.143
r_symmetry_nbd_refined	0.106
r_ncsr_local_group_3	0.102
r_ncsr_local_group_2	0.101
r_symmetry_xyhbond_nbd_refined	0.093
r_chiral_restr	0.092
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20010
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	263

Software

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