3BQ1 | pdb_00003bq1

Insertion ternary complex of Dbh DNA polymerase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IM4	PDB entries 1IM4 and 1K1Q
experimental model	PDB	1K1Q	PDB entries 1IM4 and 1K1Q

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
2.88	57.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.96	α = 90
b = 124.96	β = 90
c = 70.21	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		2007-03-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	2.7	25	99.6	0.066	24.4	6.5		15669		-0.5

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	2.7	2.75	99.1		0.523	2.1	5.1

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 1IM4 and 1K1Q	2.7	20	14437	14437	711	99.6	0.207	0.207	0.204	0.2	0.267	0.19	RANDOM	42.582

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]
0.66			0.66		-1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.03
r_dihedral_angle_3_deg	17.946
r_dihedral_angle_4_deg	13.984
r_dihedral_angle_1_deg	4.72
r_scangle_it	1.411
r_angle_refined_deg	1.242
r_scbond_it	0.823
r_mcangle_it	0.593
r_mcbond_it	0.339
r_nbtor_refined	0.301
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.127
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.071
r_metal_ion_refined	0.019
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2719
Nucleic Acid Atoms	466
Solvent Atoms	41
Heterogen Atoms	31

Software

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