4XDQ

Crystal structure of a Glycoside hydrolase family protein (Rv0315 ortholog) from Mycobacterium thermorestibile

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	MythA.18623.a.B2.PS02026 at 20.8 mg/mL against JCSG+ screen condition G5, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2, 5 mM NiCl2, 0.1 M Hepes pH 7.5, 15% PEG 3350 supplemented with 20 % EG as cryo

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.55	α = 90
b = 74.55	β = 90
c = 95.53	γ = 90

Symmetry
Space Group	P 43 21 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	CCD	MARMOSAIC 300 mm CCD		2014-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.35	50	100	0.059	0.061	28.25	14.4		59755		-3	18.076

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.39	100		0.532	0.552	5.4	14.3

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	3rq0	1.35	50	56708	2968	99.97	0.1264	0.1253	0.1479	RANDOM	14.451

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]
-0.56			-0.56		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.355
r_dihedral_angle_4_deg	24.391
r_dihedral_angle_3_deg	9.765
r_dihedral_angle_1_deg	7.272
r_sphericity_bonded	5.883
r_rigid_bond_restr	1.703
r_angle_refined_deg	1.361
r_mcangle_it	1.227
r_mcbond_it	0.961
r_mcbond_other	0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.355
r_dihedral_angle_4_deg	24.391
r_dihedral_angle_3_deg	9.765
r_dihedral_angle_1_deg	7.272
r_sphericity_bonded	5.883
r_rigid_bond_restr	1.703
r_angle_refined_deg	1.361
r_mcangle_it	1.227
r_mcbond_it	0.961
r_mcbond_other	0.96
r_angle_other_deg	0.739
r_chiral_restr	0.085
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1895
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
BALBES	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.