6YQH | pdb_00006yqh

GH146 beta-L-arabinofuranosidase bound to covalent inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OPJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	10 mg/mL enzyme treated with 200 uM inhibitor at 37C for 16 hours and subsequently mixed 1:1 with 20% PEG3350, 0.2 M ammonium formate, 170 mM arabinose, 0.1 M pH 6.0 MES

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.418	α = 90
b = 95.418	β = 90
c = 189.068	γ = 90

Symmetry
Space Group	P 43 21 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 EIGER2 X 16M		2019-09-14	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)	Rrim 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	1.41	95.42	100	0.12	1	11.7	16.2		167826

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.43	98.1		3.073	0.5	1.1	16.5

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	5OPJ	1.41	85.33	167656	8404	96.983	0.131	0.1286	0.13	0.17	0.17	20.174

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]
-0.057			-0.057		0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.863
r_dihedral_angle_4_deg	20.822
r_dihedral_angle_other_3_deg	18.239
r_dihedral_angle_3_deg	11.82
r_dihedral_angle_1_deg	6.862
r_scangle_other	3.996
r_scangle_it	3.994
r_rigid_bond_restr	3.925
r_lrange_it	3.787
r_lrange_other	3.734
r_scbond_it	3.557
r_scbond_other	3.405
r_mcangle_it	2.964
r_mcangle_other	2.964
r_mcbond_it	2.614
r_mcbond_other	2.614
r_angle_refined_deg	1.877
r_angle_other_deg	1.604
r_symmetry_nbd_refined	0.333
r_nbd_other	0.253
r_nbd_refined	0.228
r_symmetry_xyhbond_nbd_refined	0.196
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.112
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6099
Nucleic Acid Atoms
Solvent Atoms	573
Heterogen Atoms	87

Software

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