2PY5

Phi29 DNA polymerase complexed with single-stranded DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES pH 6.5, 12% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.195	α = 90
b = 200.178	β = 109.4
c = 66.989	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	ADSC QUANTUM 315		2006-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C		APS	24-ID-C

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	1.601	50	97.8	0.045	49.9	6.9	176187	172311		-3

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)
	1.601	1.66	92.2		0.44	3.7	5.5

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	copy C of 1XHX without residues 359-394	1.6	40.59	176187	163498	8614	97.83	0.16547	0.16399	0.19363	RANDOM	26.563

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]
-0.23		-0.16	-0.12		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.81
r_dihedral_angle_3_deg	12.333
r_dihedral_angle_4_deg	12.06
r_dihedral_angle_1_deg	6.049
r_scangle_it	3.044
r_mcangle_it	2.333
r_scbond_it	2.108
r_mcbond_it	1.689
r_angle_refined_deg	1.201
r_angle_other_deg	0.8
r_mcbond_other	0.486
r_symmetry_hbond_refined	0.244
r_nbd_refined	0.202
r_nbtor_refined	0.187
r_nbd_other	0.186
r_symmetry_vdw_other	0.174
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.129
r_nbtor_other	0.084
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9267
Nucleic Acid Atoms	532
Solvent Atoms	1493
Heterogen Atoms	108

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling