3DMH | pdb_00003dmh

T. Thermophilus 16S rRNA N2 G1207 methyltransferase (RsmC) in complex with AdoMet and Guanosine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch technique under oil	8.5	277	0.085 M TRIS HCl (pH 8.5), 25.5% w/v PEG4000 15% glycerol, microbatch technique under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.863	α = 90
b = 86.234	β = 90
c = 95.091	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	MAR CCD 165 mm	Slits: Variable vertical and horizontal slits. Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m.	2008-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9797	NSLS	X4C

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	1.55	30	97.8	0.066	23.8	5.7		57244

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	1.55	1.61	81.6		0.418	2.2	3.1	3603

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	SAD	THROUGHOUT	1.55	30	57244	3060	98.37	0.19518	0.19355	0.19	0.22577	0.22	RANDOM	24.107

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]
-0.13			0.86		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.099
r_dihedral_angle_4_deg	14.175
r_dihedral_angle_3_deg	12.167
r_dihedral_angle_1_deg	6.019
r_scangle_it	2.976
r_scbond_it	1.892
r_angle_refined_deg	1.361
r_mcangle_it	1.078
r_mcbond_it	0.707
r_nbtor_refined	0.304
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.15
r_symmetry_vdw_refined	0.136
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2833
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing