8R6Z | pdb_00008r6z

Polysaccharide lyase BtPL33HA (BT4410) Apo form 2

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experimental model	Other		unpublished structure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 0.1M MES pH6.0 0.1 M Ammonium chloride 20 mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.529	α = 90
b = 137.672	β = 90
c = 202.506	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 PILATUS3 6M		2021-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9999	Diamond	I24

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	2.03	113.85	90.8	0.99	6.6	5.9		73386

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	2.03	2.17			0.503	1.6

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	2.03	113.85	73385	3607	75.003	0.194	0.1912	0.1978	0.2505	0.2539	31.44

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]
-0.995			0.136		0.859

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.388
r_dihedral_angle_3_deg	16.952
r_dihedral_angle_6_deg	15.341
r_dihedral_angle_1_deg	7.535
r_lrange_it	6.731
r_lrange_other	6.726
r_scangle_it	5.714
r_scangle_other	5.713
r_scbond_it	3.856
r_scbond_other	3.856
r_mcangle_it	3.546
r_mcangle_other	3.546
r_angle_refined_deg	2.539
r_mcbond_it	2.495
r_mcbond_other	2.49
r_angle_other_deg	0.817
r_metal_ion_refined	0.25
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.224
r_nbd_other	0.208
r_symmetry_xyhbond_nbd_refined	0.204
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.194
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.111
r_ncsr_local_group_1	0.11
r_symmetry_nbtor_other	0.097
r_symmetry_xyhbond_nbd_other	0.057
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9816
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing