3PKN | pdb_00003pkn

Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KUS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	0.25 M potassium iodide, 1.9 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.91	α = 90
b = 31.384	β = 104.95
c = 52.647	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 210		2010-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9770	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50	98.8			6954	6871	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.83	89

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 (All)	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	3KUS	1.8	50.83	1	6954	6871	335	98	0.227	0.22683	0.22479	0.23	0.26933	0.27	RANDOM	30.608

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]
1.52		2.44	-1.42		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.653
r_dihedral_angle_3_deg	18.705
r_dihedral_angle_4_deg	10.305
r_dihedral_angle_1_deg	4.252
r_scangle_it	2.641
r_scbond_it	1.677
r_angle_refined_deg	1.113
r_mcangle_it	0.889
r_mcbond_it	0.586
r_nbtor_refined	0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.653
r_dihedral_angle_3_deg	18.705
r_dihedral_angle_4_deg	10.305
r_dihedral_angle_1_deg	4.252
r_scangle_it	2.641
r_scbond_it	1.677
r_angle_refined_deg	1.113
r_mcangle_it	0.889
r_mcbond_it	0.586
r_nbtor_refined	0.29
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.102
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	691
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	6

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.