2NXE | pdb_00002nxe

T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in complex with S-Adenosyl-L-Methionine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	190 mM Calcium chloride dihydrate, 95mM HEPES-Na, pH 7.5, 26.6% v/v PEG400, 5% glycerol, microbatch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.179	α = 90
b = 187.179	β = 90
c = 45.189	γ = 120

Symmetry
Space Group	H 3

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		2006-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		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	1.75	30	99.6	0.046	19.13	2.5	59737	59391		-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	1.75	1.81	99.5		0.434	2.1	2.2	5929

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 entry 2NXC	1.75	30	56389	3002	99.53	0.20265	0.20149	0.2	0.22396	0.22	RANDOM	31.865

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	32.06
r_dihedral_angle_4_deg	19.251
r_dihedral_angle_3_deg	16.893
r_dihedral_angle_1_deg	6.161
r_scangle_it	3.592
r_scbond_it	2.367
r_angle_refined_deg	1.705
r_mcangle_it	1.524
r_mcbond_it	1.006
r_xyhbond_nbd_refined	0.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.06
r_dihedral_angle_4_deg	19.251
r_dihedral_angle_3_deg	16.893
r_dihedral_angle_1_deg	6.161
r_scangle_it	3.592
r_scbond_it	2.367
r_angle_refined_deg	1.705
r_mcangle_it	1.524
r_mcbond_it	1.006
r_xyhbond_nbd_refined	0.382
r_nbtor_refined	0.308
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.195
r_symmetry_hbond_refined	0.175
r_chiral_restr	0.129
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3860
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
COMO	phasing
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.