2JC5

Apurinic Apyrimidinic (AP) endonuclease (NApe) 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	VAPOR DIFFUSION, HANGING DROP	9		24 WELL LINBRO PLATES USED FOR HANGING DROP EXPERIMENTS WITH 0.5 UL PROTEIN AND 0.5 UL WELL SOLUTION FOR THE DROPS. PROTEIN CONCENTRATION 20 MG/ML, IN 10 MM TRIS, PH 7.0 AND 100 MM NACL. THE WELL SOLUTION CONTAINED 20% PEG 20000, 0.1 M BICINE PH 9.0, 2% DIOXANE.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.156	α = 90
b = 79.511	β = 107.22
c = 41.045	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 CCD		2005-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.5	30	94.6	0.06	18.3	3.5		35560		-3	9.64

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	1.5	1.55	86.3		0.27	4.5	3.1

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-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	PDB ENTRY 1BIX	1.5	29.53	35412	1774	100	0.123	0.12	0.13	0.159	0.17	RANDOM	8.98

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]
-0.336		0.022	0.654		-0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.826
r_dihedral_angle_4_deg	13.08
r_dihedral_angle_3_deg	10.996
r_dihedral_angle_1_deg	6.191
r_scangle_it	2.868
r_mcangle_it	2.506
r_scbond_it	2.16
r_mcbond_it	1.986
r_angle_refined_deg	1.33
r_symmetry_vdw_refined	0.722
r_symmetry_hbond_refined	0.479
r_nbd_refined	0.263
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
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	2073
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	36

Software

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