3ID5 | pdb_00003id5

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	1.7M (NH4)2SO4, 50mM Na cacodylate, pH 5.6, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
5.94	79.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 265.485	α = 90
b = 265.485	β = 90
c = 129.434	γ = 90

Symmetry
Space Group	P 41 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						SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00821	SPring-8	BL41XU

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	4	50	98.5	0.139	17.5	12.3		39544

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	4	4.07	85.5		0.83	1.6	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SIRAS	THROUGHOUT	4.01	20	37665	1888	96.54	0.286	0.285	0.27	0.304	0.28	RANDOM	166.712

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]
-2.34			-2.34		4.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.74
r_dihedral_angle_3_deg	17.923
r_dihedral_angle_4_deg	16.382
r_dihedral_angle_1_deg	4.685
r_mcangle_it	1.281
r_scangle_it	1.212
r_angle_refined_deg	1.135
r_scbond_it	0.86
r_mcbond_it	0.695
r_nbtor_refined	0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.74
r_dihedral_angle_3_deg	17.923
r_dihedral_angle_4_deg	16.382
r_dihedral_angle_1_deg	4.685
r_mcangle_it	1.281
r_scangle_it	1.212
r_angle_refined_deg	1.135
r_scbond_it	0.86
r_mcbond_it	0.695
r_nbtor_refined	0.292
r_symmetry_hbond_refined	0.237
r_symmetry_vdw_refined	0.201
r_nbd_refined	0.173
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.097
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11276
Nucleic Acid Atoms	1400
Solvent Atoms
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	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.