3KUJ | pdb_00003kuj

Crystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I2T	pdb entry 1I2T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	295	1.4M ammonium sulfate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.66	26.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.217	α = 90
b = 50.802	β = 90
c = 32.121	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 210	mirrors	2008-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.9780	CHESS	F2

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	50	99.6	0.074	19.2	7.5	14288	14231	1	1

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	1.4	1.45	99.9		0.375	6.1	6.6	997

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1I2T	1.4	33.77	1	14288	14231	756	99.36	0.19713	0.19578	0.19	0.22331	0.22	RANDOM	11.223

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]
0.2			-0.21		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.185
r_dihedral_angle_4_deg	16.126
r_dihedral_angle_3_deg	14.251
r_dihedral_angle_1_deg	4.037
r_scangle_it	2.86
r_scbond_it	1.945
r_angle_refined_deg	1.249
r_mcangle_it	1.013
r_mcbond_it	0.662
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.185
r_dihedral_angle_4_deg	16.126
r_dihedral_angle_3_deg	14.251
r_dihedral_angle_1_deg	4.037
r_scangle_it	2.86
r_scbond_it	1.945
r_angle_refined_deg	1.249
r_mcangle_it	1.013
r_mcbond_it	0.662
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.18
r_chiral_restr	0.106
r_xyhbond_nbd_refined	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	698
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	10

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.