3CJR

Ribosomal protein L11 methyltransferase (PrmA) in complex with ribosomal protein L11 (K39A) and inhibitor Sinefungin.

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	8.5	277	170 mM sodium acetate trihydrate, 85 mM TRIS-HCl, 25.5 (w/v) PEG 4000, 15% (v/v) glycerol, 1 mM Sinefungin, pH 8.5, microbatch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.742	α = 90
b = 132.742	β = 90
c = 46.056	γ = 120

Symmetry
Space Group	P 65

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 4	Variable vertical and fixed horizontal slits. KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position. Mirror system consisting of two vertically stacked, fused silica, spherical mirrors, to provide vertical focusing and harmonic rejection. One of the mirrors is rhodium coated and the other is uncoated. Located ~19.7 m from source.	2007-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.9797	NSLS	X4A

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	2.05	50	99.7	0.067	18.7	3.7		27841		-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	2.05	2.12	99		0.528	2.3	3.4	5621

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	2.05	20	27841	1491	99.96	0.21636	0.21322	0.21	0.27695	0.27	RANDOM	51.919

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]
-0.33	-0.17		-0.33		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.566
r_dihedral_angle_3_deg	15.59
r_dihedral_angle_4_deg	13.497
r_dihedral_angle_1_deg	5.176
r_angle_refined_deg	1.125
r_scangle_it	0.971
r_scbond_it	0.58
r_mcangle_it	0.557
r_mcbond_it	0.314
r_nbtor_refined	0.297
r_nbd_refined	0.177
r_symmetry_hbond_refined	0.111
r_symmetry_vdw_refined	0.103
r_xyhbond_nbd_refined	0.093
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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	2791
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	27

Software

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