2JC4 | pdb_00002jc4

3'-5' exonuclease (NExo) from Neisseria Meningitidis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		PROTEIN CONCENTRATION 8.7MG/ML BUFFER: 10 MM TRIS, PH 7.0, 100 MM NACL . WELL SOLUTION: 100 MM NA CACODYLATE PH 6 200 MM NA ACETATE, 15 % PEG 8000. THE CRYSTALLISATION PLATES USED WERE CORNING ROUND BOTTOM 96 WELL PLATES. THE CRYSTALLISATION DROPS CONSISTED OF 1UL PROTEIN AND 1UL WELL SOLUTION.

Crystal Properties
Matthews coefficient	Solvent content
2.06	31.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.193	α = 90
b = 58.618	β = 90
c = 88.635	γ = 90

Symmetry
Space Group	P 21 21 21

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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1		SRS	PX14.1

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	1.9	20	97.6	0.09	24.5	6.8		19164		-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)
1	1.9	1.97	91.4		0.32	5.1

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BIX	1.9	19.96	19112	982	100	0.152	0.15	0.202	0.2	RAMDOM	16.05

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]
0.193			0.079		-0.272

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.938
r_dihedral_angle_4_deg	17.177
r_dihedral_angle_3_deg	12.594
r_dihedral_angle_1_deg	6.176
r_scangle_it	3.5
r_scbond_it	2.328
r_angle_refined_deg	1.501
r_mcangle_it	1.372
r_mcbond_it	0.783
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
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
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2028
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing