3CG7 | pdb_00003cg7

Crystal structure of cell-death related nuclease 4 (CRN-4)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	0.2M sodium formate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
4.84	74.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.474	α = 90
b = 165.379	β = 90
c = 64.263	γ = 90

Symmetry
Space Group	P 21 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 315		2006-07-01	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-09-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	0.999	NSRRC	BL13B1
2	SYNCHROTRON	NSRRC BEAMLINE BL13B1	0.978993,0.963960,0.979185	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.5	30	96.3	0.052	21.5	4.3		45644		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.56	88.6		0.426	0.426	3.01	3.8

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	MAD	THROUGHOUT	2.5	30	45644	43319	2301	96.31	0.20816	0.2061	0.2	0.24681	0.24	RANDOM	47.021

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]
-1.44			1.4		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.961
r_dihedral_angle_3_deg	16.681
r_dihedral_angle_4_deg	15.127
r_dihedral_angle_1_deg	5.515
r_rigid_bond_restr	4.678
r_sphericity_free	3.388
r_scangle_it	2.493
r_sphericity_bonded	2.011
r_scbond_it	1.558
r_mcangle_it	1.154
r_angle_refined_deg	1.145
r_mcbond_it	0.663
r_nbtor_refined	0.306
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4822
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing