2OG4

Structure of an expanded Jab1-MPN-like domain of splicing factor Prp8p from yeast

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2.5 % PEG 3350, 0.01 M CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.465	α = 90
b = 78.465	β = 90
c = 122.812	γ = 90

Symmetry
Space Group	P 42 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	MAR CCD 165 mm	mirrors	2006-10-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2006-10-04	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6
2	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	0.97890, 0.97920, 0.95000	MPG/DESY, HAMBURG	BW6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2	30	97.8	0.112	16.1	4.8	26671	26084	1	1	27.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2	2.05	96		0.618	2.1	4.8	2003

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	20	1	1	25289	24738	1315	97.82	0.20382	0.20176	0.24149	RANDOM	28.831

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]
-1.42			-1.42		2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.865
r_dihedral_angle_4_deg	18.013
r_dihedral_angle_3_deg	12.887
r_dihedral_angle_1_deg	5.961
r_scangle_it	2.364
r_scbond_it	1.444
r_mcangle_it	1.251
r_angle_refined_deg	1.186
r_mcbond_it	0.724
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.865
r_dihedral_angle_4_deg	18.013
r_dihedral_angle_3_deg	12.887
r_dihedral_angle_1_deg	5.961
r_scangle_it	2.364
r_scbond_it	1.444
r_mcangle_it	1.251
r_angle_refined_deg	1.186
r_mcbond_it	0.724
r_nbtor_refined	0.298
r_symmetry_vdw_refined	0.185
r_nbd_refined	0.182
r_xyhbond_nbd_refined	0.124
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1995
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHELXE	model building

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 R01GM133198.