6CN0

2.95 Angstrom Crystal Structure of 16S rRNA Methylase from Proteus mirabilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	292	Protein: 10.0 mg/ml, 0.3M Sodium chloride, 2mM Magnesium chloride, 0.01M HEPES (pH 7.5), Screen: 2M Ammonium Sulfate, 0.1M Sodium citrate (pH 5.6), 1% Isopropanol, Cryo: paratone

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.318	α = 90
b = 158.318	β = 90
c = 122.892	γ = 120

Symmetry
Space Group	P 61

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	C(111)	2016-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	2.95	30	99.9	0.053	0.053	0.06	0.027	25.7	4.7		36800		-3	95.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3	100		0.874	0.874	0.986	0.446	0.612	2	4.7

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	3LCU	2.95	29.98	34904	1865	99.8	0.22014	0.21789	0.26286	RANDOM	113.934

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]
0.25	0.12		0.25		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.831
r_dihedral_angle_3_deg	8.822
r_dihedral_angle_4_deg	8.808
r_long_range_B_refined	7.203
r_long_range_B_other	7.202
r_mcangle_it	3.9
r_mcangle_other	3.9
r_scangle_other	3.65
r_mcbond_it	2.28
r_mcbond_other	2.279
r_scbond_it	2.133
r_scbond_other	2.131
r_dihedral_angle_1_deg	1.773
r_angle_refined_deg	1.298
r_angle_other_deg	0.881
r_chiral_restr	0.078
r_gen_planes_refined	0.023
r_gen_planes_other	0.02
r_bond_refined_d	0.007
r_bond_other_d	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8544
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing