2VOA | pdb_00002voa

Structure of an AP Endonuclease from Archaeoglobus fulgidus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	292	HANGING-DROP METHOD AT 292 K WITH 1 MICROLITER OF RESERVOIR AND PROTEIN SOLUTION EACH. TRIS-HCL PH 8.5. PROTEIN: 17 MG/ML AF_EXO, 0.53 MM DS-DNA, 9 MM MES-NAOH PH 6, 0.28 M NACL.

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.786	α = 90
b = 60.817	β = 91.22
c = 72.349	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	MARRESEARCH	MIRRORS	2005-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	1.7	30	100	0.07	24.5	7.8		64871		-3	29.5

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	1.7	1.74	99.9		0.44	2.3	5.4

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 1AKO	1.7	29.6	63550	1314	100	0.198	0.198	0.23	0.23	0.25	RANDOM	31.56

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]
-0.56		0.17	-1.32		1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.469
r_dihedral_angle_4_deg	17.144
r_dihedral_angle_3_deg	14.12
r_dihedral_angle_1_deg	5.958
r_scangle_it	2.673
r_scbond_it	1.741
r_angle_refined_deg	1.398
r_mcangle_it	1.043
r_mcbond_it	0.675
r_nbtor_refined	0.303
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.115
r_chiral_restr	0.095
r_xyhbond_nbd_refined	0.095
r_bond_refined_d	0.012
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	4204
Nucleic Acid Atoms	404
Solvent Atoms	220
Heterogen Atoms

Software

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