6QEY | pdb_00006qey

IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	51.4% PEG1000 150 mM MOPS pH 7.0 60 mM Sodium Iodide 4% acetonitrile

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.421	α = 90
b = 32.987	β = 103.14
c = 58.721	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2013-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97949	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	37.21	97	0.113	0.993	7.28	2.74		8950			34.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	96.8		0.719	0.607	1.89	2.73

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	37.21	7377	417	96.94	0.1845	0.1812	0.19	0.2455	0.25	RANDOM	39.075

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]
-1.35		-0.22	1.43		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.538
r_dihedral_angle_4_deg	23.272
r_dihedral_angle_3_deg	16.771
r_dihedral_angle_1_deg	6.187
r_angle_refined_deg	1.866
r_angle_other_deg	1.381
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.538
r_dihedral_angle_4_deg	23.272
r_dihedral_angle_3_deg	16.771
r_dihedral_angle_1_deg	6.187
r_angle_refined_deg	1.866
r_angle_other_deg	1.381
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1283
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.