3CJT | pdb_00003cjt

Ribosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal protein L11

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NXC	pdb entries 2NXC, 2NXN
experimental model	PDB	2NXN	pdb entries 2NXC, 2NXN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	5.8	277	200mM magnesium nitrate hexahydrate, 20% w/v PEG3350, 4mM AdoMet, pH 5.8, microbatch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.822	α = 90
b = 69.943	β = 90.47
c = 379.007	γ = 90

Symmetry
Space Group	P 1 2 1

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	ADSC QUANTUM 315	Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror	2007-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9797	NSLS	X29A

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	2.3	30	96.5	0.071	25	6.7		157914		-3

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	2.3	2.38	76.7		0.364	2.7	4.6	12404

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 2NXC, 2NXN	2.3	29.74	149975	7909	96.31	0.19765	0.19442	0.19	0.2593	0.25	RANDOM	44.08

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]
0.01		-0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.514
r_dihedral_angle_4_deg	20.195
r_dihedral_angle_3_deg	17.687
r_dihedral_angle_1_deg	6.326
r_scangle_it	2.802
r_scbond_it	1.715
r_angle_refined_deg	1.538
r_mcangle_it	1.071
r_mcbond_it	0.647
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.247
r_xyhbond_nbd_refined	0.243
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.211
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
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	21338
Nucleic Acid Atoms
Solvent Atoms	1885
Heterogen Atoms	296

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing