3BQ0

Pre-insertion binary complex of Dbh DNA polymerase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG-3350, calcium acetate, glycerol, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.416	α = 90
b = 119.416	β = 90
c = 68.274	γ = 90

Symmetry
Space Group	P 41 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	ADSC QUANTUM 315		2006-10-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.9795	NSLS	X25

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	2.6	20	89.3	0.048	35.4	4.6		14027		-1

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	2.6	2.64	81.4		0.314	3.4	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 1IM4 and 1K1Q	2.6	19.9	13804	13125	679	88.15	0.21711	0.21387	0.27904	RANDOM	52.826

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]
3.07			3.07		-6.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.56
r_dihedral_angle_3_deg	18.777
r_dihedral_angle_4_deg	15.758
r_dihedral_angle_1_deg	5.532
r_scangle_it	1.466
r_angle_refined_deg	1.246
r_scbond_it	0.859
r_mcangle_it	0.698
r_mcbond_it	0.398
r_metal_ion_refined	0.311
r_nbtor_refined	0.306
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.203
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.078
r_bond_refined_d	0.009
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_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	2704
Nucleic Acid Atoms	462
Solvent Atoms	110
Heterogen Atoms	1

Software

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