3UCG

Crystal structure of a RNA binding domain of polyadenylate-binding protein (PABPN1) from Homo sapiens at 1.95 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	2.0M (NH4)2SO4, 2.0% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.678	α = 90
b = 92.678	β = 90
c = 92.678	γ = 90

Symmetry
Space Group	I 2 3

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)	2011-07-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97925,0.97894	SSRL	BL11-1

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	1.95	29.307	99.2	0.045	18.08			9771		-3	37.166

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	1.95	2.02	97.2		0.771	1.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.95	29.307	9767	470	99.51	0.165	0.1629	0.2096	RANDOM	53.3522

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.992
r_dihedral_angle_3_deg	15.035
r_torsion_it	11.522
r_dihedral_angle_4_deg	9.444
r_angle_it	8.617
r_bond_it	6.535
r_angle_others	5.182
r_dihedral_angle_1_deg	4.427
r_angle_refined_deg	1.714
r_bond_other	1.586

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.992
r_dihedral_angle_3_deg	15.035
r_torsion_it	11.522
r_dihedral_angle_4_deg	9.444
r_angle_it	8.617
r_bond_it	6.535
r_angle_others	5.182
r_dihedral_angle_1_deg	4.427
r_angle_refined_deg	1.714
r_bond_other	1.586
r_angle_other_deg	0.995
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	677
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	30

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.