9YWN | pdb_00009ywn

Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase

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	4.6	289	0.17 M ammonium acetate, 0.085 M sodium acetate HCl pH 4.6, 25.5 percent PEG 4000 and 15 percent glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.307	α = 90
b = 133.392	β = 101.544
c = 137.7	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 XE 9M		2024-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9857	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.92	50.21	99.6	0.131	0.072	0.994	9.4	3.3		239756			32.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.95	96.2		1.157	0.649	0.403	0.89	2.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.916	48.949	239538	11805	98.983	0.17	0.1686	0.1772	0.205	0.2116	RANDOM	25.988

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]
0.063		0.787	-0.577		0.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.504
r_dihedral_angle_3_deg	13.115
r_dihedral_angle_2_deg	7.418
r_dihedral_angle_1_deg	6.969
r_lrange_it	6.811
r_lrange_other	6.74
r_scangle_it	4.895
r_scangle_other	4.895
r_mcangle_it	3.651
r_mcangle_other	3.651
r_scbond_it	3.14
r_scbond_other	3.14
r_mcbond_it	2.435
r_mcbond_other	2.434
r_angle_refined_deg	1.597
r_angle_other_deg	0.546
r_symmetry_xyhbond_nbd_refined	0.296
r_nbd_other	0.223
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.211
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.17
r_metal_ion_refined	0.151
r_symmetry_xyhbond_nbd_other	0.123
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19950
Nucleic Acid Atoms
Solvent Atoms	1630
Heterogen Atoms	267

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing