2PLW

Crystal structure of a ribosomal RNA methyltransferase, putative, from Plasmodium falciparum (PF13_0052).

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	298	24% PEG 3350, 0.1 M (NH4)2SO4, 0.1 M Bis-Tris pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.595	α = 90
b = 59.798	β = 90
c = 71.295	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	ADSC QUANTUM 270		2007-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91770	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	50	98.5	0.073	0.065	9.9	6.8	20472	20472

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	87.9		0.324	0.284	3.7	5.4	1782

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2NYU	1.7	45.83	20366	20366	1042	98.65	0.205	0.205	0.202	0.247	RANDOM	20.927

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.665
r_dihedral_angle_4_deg	19.574
r_dihedral_angle_3_deg	15.315
r_dihedral_angle_1_deg	6.522
r_scangle_it	3.759
r_scbond_it	2.562
r_mcangle_it	1.684
r_angle_refined_deg	1.522
r_mcbond_it	1.043
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.665
r_dihedral_angle_4_deg	19.574
r_dihedral_angle_3_deg	15.315
r_dihedral_angle_1_deg	6.522
r_scangle_it	3.759
r_scbond_it	2.562
r_mcangle_it	1.684
r_angle_refined_deg	1.522
r_mcbond_it	1.043
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.233
r_symmetry_hbond_refined	0.228
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1472
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

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.