8R72 | pdb_00008r72

Polysaccharide lyase BtPL33HA (BT4410) Y291A with HA dp4 collected at 1.33 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	20 % PEG 6000 0.1 M MES pH 6.0 0.1 M Ammonium chloride 20 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.87	α = 90
b = 137.4	β = 90
c = 203.33	γ = 90

Symmetry
Space Group	P 21 21 21

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		2022-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.33	Diamond	I04

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	2.58	53.87	100	0.989	8.4	6.5		48609

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	2.58	2.66			0.574	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	2.58	52.128	48536	2536	99.938	0.222	0.2186	0.22	0.2807	0.2833	48.173

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]
3.395			-1.385		-2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.712
r_dihedral_angle_6_deg	14.983
r_dihedral_angle_2_deg	8.255
r_lrange_it	8.153
r_lrange_other	8.153
r_dihedral_angle_1_deg	7.688
r_scangle_it	6.369
r_scangle_other	6.369
r_mcangle_it	5.985
r_mcangle_other	5.984
r_scbond_it	4.107
r_scbond_other	4.107
r_mcbond_it	3.945
r_mcbond_other	3.944
r_angle_refined_deg	1.492
r_angle_other_deg	0.479
r_nbd_other	0.242
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.155
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.131
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.067
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9821
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	108

Software

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