1XQO | pdb_00001xqo

Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	PEG 4000, HEPES-NaOH, NaCl, Dithio threitol., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.89	α = 90
b = 97.69	β = 90
c = 36.1	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	MARRESEARCH		2003-10-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.03	57.74	93.7	0.07	0.058	11.6	5	587271	116782		-3	13

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.03	1.1	78.1		0.468	2.5	3.9	17208

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 (All)	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	1.03	40	110906	110906	5880	93.76	0.15889	0.15889	0.15762	0.21	0.18275	0.23	RANDOM	15.567

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]
0.09			-0.06		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.34
r_dihedral_angle_4_deg	15.511
r_dihedral_angle_3_deg	12.177
r_sphericity_free	7.537
r_dihedral_angle_1_deg	5.066
r_scangle_it	4.5
r_sphericity_bonded	3.732
r_scbond_it	3.657
r_mcangle_it	2.622
r_angle_other_deg	2.496
r_mcbond_it	2.297
r_rigid_bond_restr	1.726
r_angle_refined_deg	1.689
r_mcbond_other	1.034
r_symmetry_vdw_other	0.36
r_nbd_refined	0.224
r_symmetry_vdw_refined	0.209
r_nbd_other	0.182
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.12
r_symmetry_hbond_refined	0.096
r_nbtor_other	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2054
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
SHARP	phasing