7OKR | pdb_00007okr

Catalytic domain from the Aliivibrio salmonicida lytic polysaccharide monooxygenase AsLPMO10B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293.15	0.1 M phosphate/citrate pH 4.2, 40 % PEG 300

Crystal Properties
Matthews coefficient	Solvent content
3.41	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.003	α = 90
b = 71.003	β = 90
c = 100.203	γ = 120

Symmetry
Space Group	P 65

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	Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)	2019-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976254	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.35	33.46	99.9	0.022	0.999	15.3	18.2		62730

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.4	99.7		0.585	0.545	0.9	9.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4YN2	1.35	33.46	62414	3085	99.531	0.14	0.1388	0.14	0.1624	0.16	27.772

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]
1.687	0.844		1.687		-5.474

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.951
r_dihedral_angle_4_deg	15.646
r_dihedral_angle_3_deg	11.894
r_scbond_it	9.175
r_scbond_other	9.171
r_scangle_it	7.092
r_scangle_other	7.089
r_dihedral_angle_1_deg	6.902
r_rigid_bond_restr	5.131
r_lrange_it	4.754
r_lrange_other	4.742
r_mcangle_other	3.205
r_mcangle_it	3.176
r_mcbond_it	2.755
r_mcbond_other	2.686
r_angle_refined_deg	1.862
r_angle_other_deg	1.623
r_symmetry_xyhbond_nbd_refined	0.223
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.174
r_nbd_other	0.135
r_metal_ion_refined	0.111
r_chiral_restr	0.103
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building