3NGO | pdb_00003ngo

Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.1M Hepes, pH 7.5, 1.1M ammonium tartrate, 0.2M NDSB-201, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.373	α = 90
b = 77.373	β = 90
c = 167.177	γ = 120

Symmetry
Space Group	P 32 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	MARMOSAIC 225 mm CCD		2009-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9796	SSRF	BL17U

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	2.2	50	99.7	0.066	52.7	10.5	30308	30217		-3

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)
	2.2	2.24	99.2		0.418	4.7	9.2	1466

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.2	50	28753	28627	1522	99.56	0.21718	0.21475	0.2122	0.26314	0.2607	RANDOM	45.014

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]
-1.21	-0.61		-1.21		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.322
r_dihedral_angle_4_deg	18.056
r_dihedral_angle_3_deg	17.858
r_dihedral_angle_1_deg	7.008
r_scangle_it	4.506
r_scbond_it	2.75
r_mcangle_it	1.898
r_angle_refined_deg	1.629
r_mcbond_it	1.017
r_chiral_restr	0.116
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2722
Nucleic Acid Atoms	54
Solvent Atoms	112
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling