Experiment: 1BPY

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9ICW	PDB ENTRY 9ICW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5		PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING A RESERVOIR CONTAINING 16.0% PEG 3350, 180 MM SODIUM ACETATE, AND 50 MM HEPES, PH 7.5., VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.543	α = 90
b = 79.817	β = 107.11
c = 54.942	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	IMAGE PLATE	MARRESEARCH	MIRRORS	1996-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	20	95	0.086		2.6		21036

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	2.2	2.28	84.8		0.18

Refinement

Statistics
Diffraction ID	Structure Solution 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 (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 9ICW	2.2	20	21036	21036	2079	95.4	0.227	0.232	0.33

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
t_dihedral_angle_d	22.1
t_it	6.5
t_angle_deg	3
t_bond_d	0.02
t_nbd	0.016
t_trig_c_planes	0.015
t_gen_planes	0.006
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2614
Nucleic Acid Atoms	631
Solvent Atoms	321
Heterogen Atoms	31

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MERLOT	phasing
TNT	refinement