3HJW | pdb_00003hjw

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	303	0.8 M KCl, 0.15 M Mg Acetate, 8% (w/v) PEG 6000, pH 6.5, vapor diffusion, hanging drop, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.013	α = 90
b = 63.026	β = 90
c = 85.447	γ = 90

Symmetry
Space Group	P 21 21 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		2008-12-12	M	SINGLE WAVELENGTH
2	1		CCD	MARMOSAIC 225 mm CCD		2008-12-12

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)	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	2.15	50	91.3	0.079	20.968	6.1		51141

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	2.15	2.23	51.1		0.592		1.8	2806

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 2HVY	2.35	46.52	42200	1807	98.73	0.218	0.217	0.21	0.248	0.24	RANDOM	37.351

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]
-1.18			0.17		1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.184
r_dihedral_angle_4_deg	17.943
r_dihedral_angle_3_deg	17.364
r_dihedral_angle_1_deg	5.606
r_scangle_it	2.457
r_scbond_it	1.516
r_angle_refined_deg	1.397
r_mcangle_it	0.94
r_mcbond_it	0.467
r_metal_ion_refined	0.376

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.184
r_dihedral_angle_4_deg	17.943
r_dihedral_angle_3_deg	17.364
r_dihedral_angle_1_deg	5.606
r_scangle_it	2.457
r_scbond_it	1.516
r_angle_refined_deg	1.397
r_mcangle_it	0.94
r_mcbond_it	0.467
r_metal_ion_refined	0.376
r_nbtor_refined	0.295
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.147
r_symmetry_vdw_refined	0.11
r_chiral_restr	0.077
r_symmetry_hbond_refined	0.057
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3964
Nucleic Acid Atoms	1515
Solvent Atoms	99
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	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.