5L0Z | pdb_00005l0z

Crystal Structure of AdoMet bound rRNA methyltransferase from Sinorhizobium meliloti

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	300	5mM Cobalt chloride , 5mM Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 9% wt/vol polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.855	α = 90
b = 82.896	β = 90
c = 108.806	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	IMAGE PLATE	RIGAKU RAXIS IV		2015-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.542

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	2.9	65.94	100	0.86	28.51	6.7		13571

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	2.9	65.94	12403	634	96.23	0.19437	0.19087	0.195	0.26498	0.2614	RANDOM	56.424

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]
0.54			-0.89		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.897
r_dihedral_angle_4_deg	19.716
r_dihedral_angle_3_deg	18.907
r_dihedral_angle_1_deg	7.549
r_long_range_B_refined	5.616
r_long_range_B_other	5.615
r_scangle_other	3.491
r_mcangle_it	3.404
r_mcangle_other	3.404
r_scbond_it	2.086
r_scbond_other	2.085
r_mcbond_it	1.957
r_mcbond_other	1.955
r_angle_refined_deg	1.667
r_angle_other_deg	1.015
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	3951
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	68

Software

Software
Software Name	Purpose
HKL-3000	data processing
HKL-3000	data scaling
REFMAC	refinement