8H25 | pdb_00008h25

Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES-NaOH buffer (pH 7.5), 10% (v/v) 2-propanol, and 200 g/L polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.384	α = 90
b = 110.998	β = 90.015
c = 120.337	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 EIGER X 16M		2017-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	2.29	45.9	99.7	0.085	0.998	13.24	3.79		108220

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	2.29	2.43			0.768	2.38

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	4E8D	2.295	45.9	108219	5374	99.618	0.197	0.1947	0.18	0.232	0.21	43.496

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]
33.108		-16.524	-10.218		-22.891

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.503
r_dihedral_angle_3_deg	13.583
r_dihedral_angle_1_deg	6.584
r_lrange_it	4.952
r_lrange_other	4.944
r_dihedral_angle_2_deg	4.791
r_mcangle_it	3.319
r_mcangle_other	3.319
r_scangle_it	3.179
r_scangle_other	3.179
r_mcbond_it	2.219
r_mcbond_other	2.219
r_scbond_it	2.077
r_scbond_other	2.076
r_angle_refined_deg	0.886
r_angle_other_deg	0.317
r_nbd_other	0.223
r_nbd_refined	0.195
r_symmetry_nbd_other	0.188
r_symmetry_nbd_refined	0.181
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.128
r_ncsr_local_group_1	0.081
r_ncsr_local_group_3	0.079
r_ncsr_local_group_6	0.079
r_ncsr_local_group_4	0.078
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_2	0.051
r_ncsr_local_group_5	0.051
r_chiral_restr	0.045
r_symmetry_xyhbond_nbd_other	0.037
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19016
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	108

Software

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