3HJY

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	303	2.0mM CoCl2, 30mM CaCl2, 2.0mM Spermine, 2.0M LiCl, pH 6.5, vapor diffusion, hanging drop, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.72	59.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 238.341	α = 90
b = 238.341	β = 90
c = 127.369	γ = 120

Symmetry
Space Group	P 62 2 2

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	MARMOSAIC 300 mm CCD		2008-03-16	M	SINGLE WAVELENGTH
2	1		CCD	MARMOSAIC 225 mm CCD		2008-03-16

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 22-BM		APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.65	49.33					22492

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2EY4	3.65	49.33	22492	1208	97.8	0.277	0.276	0.306	RANDOM	132.735

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]
-6.76	-3.38		-6.76		10.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.603
r_dihedral_angle_4_deg	22.314
r_dihedral_angle_3_deg	21.598
r_dihedral_angle_1_deg	6.922
r_scangle_it	2.27
r_mcangle_it	1.656
r_angle_refined_deg	1.505
r_scbond_it	1.237
r_mcbond_it	0.911
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.603
r_dihedral_angle_4_deg	22.314
r_dihedral_angle_3_deg	21.598
r_dihedral_angle_1_deg	6.922
r_scangle_it	2.27
r_mcangle_it	1.656
r_angle_refined_deg	1.505
r_scbond_it	1.237
r_mcbond_it	0.911
r_nbtor_refined	0.312
r_nbd_refined	0.239
r_symmetry_vdw_refined	0.227
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2989
Nucleic Acid Atoms	1271
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction

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 R01GM133198.