3VKE | pdb_00003vke

Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZTG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293	0.1M phosphate-citrate, 40%(v/v) PEG 300, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.597	α = 90
b = 114.887	β = 93.73
c = 43.429	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	CCD	ADSC QUANTUM 315r		2010-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9801	Australian Synchrotron	MX1

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	1.77	38.51		0.09	7.9	3.2		36143		3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1ZTG	1.77	27.16	35997	1808	100	0.1636	0.161	0.1635	0.2134	0.1628	RANDOM	31.5288

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]
-2.36		-1.68	1.63		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.111
r_dihedral_angle_4_deg	25.703
r_dihedral_angle_3_deg	16.23
r_scangle_it	8.277
r_scbond_it	5.85
r_dihedral_angle_1_deg	5.433
r_mcangle_it	3.962
r_rigid_bond_restr	3.115
r_mcbond_it	2.409
r_angle_refined_deg	2.243

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.111
r_dihedral_angle_4_deg	25.703
r_dihedral_angle_3_deg	16.23
r_scangle_it	8.277
r_scbond_it	5.85
r_dihedral_angle_1_deg	5.433
r_mcangle_it	3.962
r_rigid_bond_restr	3.115
r_mcbond_it	2.409
r_angle_refined_deg	2.243
r_chiral_restr	0.157
r_bond_refined_d	0.027
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2237
Nucleic Acid Atoms	388
Solvent Atoms	71
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing

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.