6Y2K

Crystal structure of beta-galactosidase from the psychrophilic Marinomonas ef1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	294	0.5 M NaCl, 100 mM Na-citrate, 2% ethylene imine polymer.

Crystal Properties
Matthews coefficient	Solvent content
4	69.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.332	α = 90
b = 133.332	β = 90
c = 232.574	γ = 120

Symmetry
Space Group	P 63 2 2

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 S 6M		2018-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.87313	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	116.29	100	0.255	10.9	29.4		96335

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	99.7		0.674		33.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1KWG	1.9	116.29	87612	4630	95.79	0.164	0.1627	0.1888	RANDOM	20.48

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]
0.69	0.34		0.69		-2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.814
r_dihedral_angle_4_deg	13.347
r_dihedral_angle_3_deg	12.631
r_dihedral_angle_1_deg	5.989
r_angle_refined_deg	1.249
r_angle_other_deg	0.922
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.814
r_dihedral_angle_4_deg	13.347
r_dihedral_angle_3_deg	12.631
r_dihedral_angle_1_deg	5.989
r_angle_refined_deg	1.249
r_angle_other_deg	0.922
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5244
Nucleic Acid Atoms
Solvent Atoms	999
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.