6YVE

Glycogen phosphorylase b in complex with pelargonidin 3-O-beta-D-glucoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.8	289	10mM BES buffer pH 6.7

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.147	α = 90
b = 126.147	β = 90
c = 115.522	γ = 90

Symmetry
Space Group	P 43 21 2

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		2019-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	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	2.1	126.15	99.9	0.085	0.998	14.7	9.3		54889

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	2.1	2.16			0.53	0.95

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	NONE	1GPb	2.1	126.15	54817	2646	99.88	0.171	0.1685	0.2263	40.882

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]
-0.016			-0.016		0.033

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.115
r_dihedral_angle_4_deg	22.374
r_dihedral_angle_3_deg	17.79
r_lrange_it	7.356
r_lrange_other	7.356
r_dihedral_angle_1_deg	6.909
r_scangle_it	5.779
r_scangle_other	5.779
r_mcangle_it	4.102
r_mcangle_other	4.101
r_scbond_it	3.977
r_scbond_other	3.976
r_mcbond_it	3.084
r_mcbond_other	3.084
r_angle_other_deg	2.294
r_angle_refined_deg	1.548
r_nbd_other	0.235
r_symmetry_nbd_other	0.22
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.195
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.144
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.071
r_bond_other_d	0.035
r_gen_planes_other	0.022
r_gen_planes_refined	0.016
r_symmetry_xyhbond_nbd_other	0.013
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6597
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	50

Software

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