6S0M | pdb_00006s0m

Structural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulence

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		277	protein concentration of 14 mg/mL in 0.1M HEPES pH 7.5, 10% w/v polyethylene glycol 8,000, 8% v/v ethylene glycol. Crystals of the complex of RNase AS with GMP were prepared by soaking crystals of native protein in a solution containing GMP at 20 mM.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.464	α = 90
b = 77.068	β = 90
c = 104.572	γ = 90

Symmetry
Space Group	P 21 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	CCD	RIGAKU SATURN 944		2018-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	Cu FINE FOCUS	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2	30	99.9	20.2	6.9		23972

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	30	21440	1150	94.36	0.18104	0.17787	0.18	0.24161	0.24	RANDOM	30.917

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]
-0.1			-0.12		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.793
r_dihedral_angle_4_deg	19.774
r_dihedral_angle_3_deg	15.42
r_dihedral_angle_1_deg	6.48
r_scangle_it	4.985
r_scbond_it	3.256
r_mcangle_it	2.285
r_angle_refined_deg	1.95
r_mcbond_it	1.286
r_chiral_restr	0.161
r_bond_refined_d	0.024
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2635
Nucleic Acid Atoms	24
Solvent Atoms	343
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing