8R73 | pdb_00008r73

Polysaccharide lyase BcPL33HA (BcellWH2_04512) Apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	10 % PEG 8000 8 % Ethylene glycol 0.1 M HEPES pH 7.5 28 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.63	α = 90
b = 91.39	β = 109.28
c = 84.77	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 EIGER X 16M		2023-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.11	40.01	99.7	1	10.8	6.7		42837

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	2.11	2.17			0.7	1.5

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	2.11	40.008	42836	2098	99.721	0.192	0.1888	0.1864	0.2502	0.2461	42.933

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]
0.029		0.781	1.831		-1.933

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.934
r_dihedral_angle_3_deg	14.869
r_dihedral_angle_2_deg	11.723
r_lrange_other	7.966
r_lrange_it	7.955
r_dihedral_angle_1_deg	7.155
r_scangle_it	6.721
r_scangle_other	6.721
r_mcangle_other	4.813
r_mcangle_it	4.812
r_scbond_it	4.791
r_scbond_other	4.79
r_mcbond_it	3.774
r_mcbond_other	3.771
r_angle_refined_deg	1.826
r_angle_other_deg	0.613
r_nbd_refined	0.215
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.16
r_xyhbond_nbd_refined	0.156
r_symmetry_nbd_refined	0.153
r_nbd_other	0.138
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.081
r_gen_planes_refined	0.009
r_bond_refined_d	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	4981
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing