3GO8 | pdb_00003go8

MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-loop deletion complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F5O	2F5O protein part only

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	PEG 8K, sodium cacodylate, glycerol, pH 7.0, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.244	α = 90
b = 92.655	β = 90
c = 105.246	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 QUANTUM 315		2006-08-17		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

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	1.89	50	98.7	0.101	15.897	5.6		35790

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	1.89	1.96	100		0.49		5.5	3555

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2F5O protein part only	1.89	32.38	34033	1685	95.19	0.187	0.185	0.1858	0.218	RANDOM	28.86

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.731
r_dihedral_angle_4_deg	15.886
r_dihedral_angle_3_deg	13.905
r_dihedral_angle_1_deg	5.453
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	2.631
SIDE-CHAIN BOND REFINED ATOMS (A''2)	1.693
r_angle_refined_deg	1.347
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	1.168
MAIN-CHAIN BOND REFINED ATOMS (A''2)	0.741
r_nbtor_refined	0.304
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.171
r_symmetry_vdw_refined	0.14
r_xyhbond_nbd_refined	0.12
CHIRAL-CENTER RESTRAINTS (A''3)	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1963
Nucleic Acid Atoms	575
Solvent Atoms	244
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing