9WVU | pdb_00009wvu

Carbohydrate-bound structure of alpha-glucan phosphorylase from Crocosphaera subtropica ATCC 51142

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-B1WXW6-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	45% (w/v) PEG 400, 0.1M Tris-HCl pH 8.0, 0.2M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 267.238	α = 90
b = 267.238	β = 90
c = 204.452	γ = 120

Symmetry
Space Group	H 3 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 PILATUS3 6M		2023-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	2.7	93.5	100	0.074	0.083	0.038	0.799	8.2	4.9		149465

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	2.7	2.85	100		0.36	0.406	0.187	0.762	2.1	4.7

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	2.7	50.005	76445	3786	99.959	0.176	0.1738	0.1799	0.2267	0.2282	49.587

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]
0.008	0.004		0.008		-0.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.574
r_dihedral_angle_4_deg	18.847
r_dihedral_angle_3_deg	18.306
r_lrange_other	7.796
r_lrange_it	7.795
r_dihedral_angle_1_deg	7.125
r_scangle_it	6.356
r_scangle_other	6.356
r_mcangle_it	5.374
r_mcangle_other	5.374
r_scbond_it	4.333
r_scbond_other	4.332
r_mcbond_it	3.765
r_mcbond_other	3.765
r_angle_refined_deg	1.667
r_angle_other_deg	1.268
r_nbd_other	0.207
r_nbd_refined	0.206
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.153
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13172
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	328

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing