1YLS | pdb_00001yls

Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	PEG400, 2-methyl-2,4-pentadiol, sodium HEPES, magnesim chloride, sodium chloride, rubidium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.99	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.873	α = 90
b = 43.269	β = 106.19
c = 79.928	γ = 90

Symmetry
Space Group	P 1 21 1

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 315	cylindrical platinum-coated silicon mirror	2004-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.979	NSLS	X25

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	3	30	99.3	0.084	11.2	3.6	10784	10709

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	3	3.11	98.2		0.52	2.6	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	3	20	10523	9979	502	99.6	0.21	0.21006	0.20881	0.21	0.23429	0.23	RANDOM	23.537

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]
1.9		-1.04	-3.88		1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.377
r_scbond_it	1.658
r_angle_refined_deg	1.538
r_angle_other_deg	1.44
r_xyhbond_nbd_other	0.62
r_nbd_other	0.291
r_symmetry_vdw_other	0.234
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.186
r_xyhbond_nbd_refined	0.186

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.377
r_scbond_it	1.658
r_angle_refined_deg	1.538
r_angle_other_deg	1.44
r_xyhbond_nbd_other	0.62
r_nbd_other	0.291
r_symmetry_vdw_other	0.234
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.186
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.171
r_nbtor_other	0.092
r_chiral_restr	0.087
r_bond_refined_d	0.016
r_gen_planes_other	0.014
r_gen_planes_refined	0.009
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	2106
Solvent Atoms	83
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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.