8QQH

Structure of beta-galactosidase from Desulfurococcus amyloliticus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		cryoEM structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	PEG3350, 0.1M NaCitrate

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.227	α = 90
b = 140.763	β = 90
c = 207.773	γ = 90

Symmetry
Space Group	P 2 21 21

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		2021-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9000	SPring-8	BL41XU

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	2.15	50	98.8	0.99	17.6	12.5		128459

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	2.15	2.19			0.75

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.15	15	127967	6351	98.397	0.168	0.1654	0.2114	42.007

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]
0.008			0.14		-0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.234
r_dihedral_angle_4_deg	20.712
r_dihedral_angle_3_deg	16.422
r_lrange_other	8.356
r_lrange_it	8.352
r_dihedral_angle_1_deg	8.196
r_scangle_it	6.618
r_scangle_other	6.618
r_mcangle_it	4.864
r_mcangle_other	4.864
r_scbond_it	4.436
r_scbond_other	4.436
r_mcbond_it	3.507
r_mcbond_other	3.506
r_angle_refined_deg	1.643
r_angle_other_deg	1.255
r_symmetry_xyhbond_nbd_refined	0.223
r_nbd_refined	0.197
r_symmetry_nbd_other	0.186
r_nbd_other	0.179
r_symmetry_nbd_refined	0.17
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.156
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.053
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15709
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms

Software

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