Experiment: 9HQW

Crystal structure of GH19 domain of D29-LysA (Form I)

X-RAY DIFFRACTION

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		293	0.1 M (DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Serine and DL-Lysine monohydrochloride) 0.1 M (Imidazole and untitrated MES) pH 6.5 37.5% w/v (MPD, PEG 1000 and PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.273	α = 90
b = 44.758	β = 126.13
c = 69.656	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 6M		2023-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.63	45.49	98.4	0.059	0.998	14.2	3.6		27799			17.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.66			0.597	0.816

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.63	45.49	1.34	27776	1420	98.36	0.1791	0.1774	0.1864	0.2112	0.2153	25.28

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.061
f_angle_d	0.8771
f_chiral_restr	0.0497
f_plane_restr	0.0086
f_bond_d	0.0061

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1507
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	21

Software

Software
Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing
autoPROC	data processing