8Z47 | pdb_00008z47

Beta-galactosidase from Bacteroides xylanisolvens (ligand-free)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8Z43

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	potassium thiocyanate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.831	α = 90
b = 163.831	β = 90
c = 50.857	γ = 90

Symmetry
Space Group	I 4

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 PILATUS3 6M		2021-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.86	41.78	100	0.996	10.3	6.6		57035

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	1.86	1.9			0.711	2.2

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.86	41.779	57030	2889	99.928	0.194	0.1925	0.1998	0.2265	0.2322	32.324

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
r_dihedral_angle_2_deg	17.239
r_dihedral_angle_6_deg	15.271
r_dihedral_angle_3_deg	14.338
r_dihedral_angle_1_deg	6.953
r_lrange_it	6.749
r_lrange_other	6.748
r_scangle_it	5.604
r_scangle_other	5.603
r_scbond_it	3.827
r_scbond_other	3.826
r_mcangle_it	3.705
r_mcangle_other	3.705
r_mcbond_it	2.831
r_mcbond_other	2.831
r_angle_refined_deg	1.684
r_angle_other_deg	0.905
r_nbd_refined	0.214
r_symmetry_nbd_other	0.208
r_nbd_other	0.189
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_refined	0.137
r_symmetry_nbd_refined	0.1
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.085
r_gen_planes_other	0.012
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_symmetry_xyhbond_nbd_other	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4015
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	12

Software

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