1N7B | pdb_00001n7b

RIP-Radiation-damage Induced Phasing

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	1 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.77	30.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.247	α = 90
b = 51.154	β = 90
c = 70.834	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 4		2002-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	1.4	20	99.3	0.095	10.99	4.25	22939	22939		-3	6.4

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	1.48	98.1		0.465	3.1	4.24	3438

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	RIP - Radiation-damage Induced Phasing	THROUGHOUT	1.4	20	-3	22939	22939	1148	99.44	0.15453	0.15453	0.15216	0.19949	RANDOM	9.645

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]
-0.24			-0.01		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	5.791
r_sphericity_free	4.347
r_scangle_it	3.844
r_scbond_it	3.131
r_rigid_bond_restr	2.128
r_angle_refined_deg	1.935
r_nbd_refined	0.412
r_symmetry_hbond_refined	0.185
r_symmetry_vdw_refined	0.138
r_xyhbond_nbd_refined	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	5.791
r_sphericity_free	4.347
r_scangle_it	3.844
r_scbond_it	3.131
r_rigid_bond_restr	2.128
r_angle_refined_deg	1.935
r_nbd_refined	0.412
r_symmetry_hbond_refined	0.185
r_symmetry_vdw_refined	0.138
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.108
r_gen_planes_refined	0.021
r_bond_refined_d	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1024
Solvent Atoms	181
Heterogen Atoms	31

Software

Software
Software Name	Purpose
ProDC	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
XDS	data scaling

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.