2P5G

Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.628	α = 90
b = 122.272	β = 96.45
c = 163.871	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	MARMOSAIC 300 mm CCD	mirrors	2006-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97857	APS	23-ID-D

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	2.8	50	98.5	0.085	14.3	3.4	125168	125168

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)
	2.8	2.9	87.7		0.402	2.6	3.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Isomorphous Replacement	THROUGHOUT	1RV2	2.8	30	101465	10837	88.41	0.24013	0.23422	0.29524	RANDOM	73.922

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]
-0.03		3.35	-1.66		2.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.238
r_dihedral_angle_3_deg	17.767
r_dihedral_angle_4_deg	17.381
r_dihedral_angle_1_deg	5.042
r_scangle_it	1.484
r_angle_refined_deg	1.062
r_scbond_it	0.902
r_mcangle_it	0.788
r_mcbond_it	0.477
r_nbtor_refined	0.304
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.181
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26440
Nucleic Acid Atoms	2336
Solvent Atoms	403
Heterogen Atoms

Software

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