3KUR

Crystal structure of the MLLE domain of poly(A)-binding protein

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	6.3	295	1.3M ammonium sulfate, 0.5M lithium sulfate, 5% glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.977	α = 90
b = 146.977	β = 90
c = 83.055	γ = 90

Symmetry
Space Group	P 43 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	2009-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.9950	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	2.5	103.7	96.7	0.076	23.1	6.3	30434	29430	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	2.5	2.57	73.5		0.4	2.8	5.4	1602

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1I2T	2.5	50	1	30434	29430	1558	96.71	0.21841	0.21566	0.27224	RANDOM	33.041

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]
1.31			1.31		-2.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.352
r_dihedral_angle_3_deg	22.719
r_dihedral_angle_4_deg	20.015
r_dihedral_angle_1_deg	5.385
r_scangle_it	3.804
r_scbond_it	2.239
r_angle_refined_deg	1.676
r_mcangle_it	1.251
r_mcbond_it	0.77
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.352
r_dihedral_angle_3_deg	22.719
r_dihedral_angle_4_deg	20.015
r_dihedral_angle_1_deg	5.385
r_scangle_it	3.804
r_scbond_it	2.239
r_angle_refined_deg	1.676
r_mcangle_it	1.251
r_mcbond_it	0.77
r_nbtor_refined	0.315
r_nbd_refined	0.253
r_symmetry_vdw_refined	0.243
r_xyhbond_nbd_refined	0.173
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.117
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4384
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	5

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.