4BJS | pdb_00004bjs

Crystal structure of the Rif1 C-terminal domain (Rif1-CTD) from Saccharomyces cerevisiae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		14-MER POLY-ALA IDEALIZED ALPHA-HELIX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				20% (W/V) PEG 3000, 200 MM NACL, 100 HEPES/NAOH PH 7.5. PROTEIN WAS TREATED WITH 0.003% TRYPSIN IMMEDIATELY PRIOR TO CRYSTALLIZATION.

Crystal Properties
Matthews coefficient	Solvent content
2.1	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.789	α = 87.41
b = 34.842	β = 79.89
c = 46.214	γ = 82.31

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2011-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA		SLS	X06DA

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	1.94	45.5	96.4	0.08	11.2	2.2		15001		-3	17.66

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	1.94	1.95	73.6		0.36	2.1	2.1

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	DIRECT METHODS	THROUGHOUT	14-MER POLY-ALA IDEALIZED ALPHA-HELIX	1.94	17.26	14980	751	95.82	0.1721	0.1708	0.18	0.1963	0.22	RANDOM	21.39

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]
1.9066	0.1192	1.0919	1.7468	-0.3853	-3.6534

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	3.76
t_other_torsion	3.04
t_angle_deg	0.89
t_bond_d	0.007
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	3.76
t_other_torsion	3.04
t_angle_deg	0.89
t_bond_d	0.007
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1714
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
Arcimboldo	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.