2PYL | pdb_00002pyl

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XHX	copy c of 1XHX without residues 359-394

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	293	100 mM CHES, 15-20% PEG 8000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.922	α = 90
b = 78.199	β = 90
c = 157.813	γ = 90

Symmetry
Space Group	P 21 21 21

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		2005-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.00003	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	2.2	50	97	0.166	8.9	4.8	37873	36737		-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)
	2.2	2.28	83.7		0.85	1.2	2.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	copy c of 1XHX without residues 359-394	2.2	40.42	37856	33015	3649	96.86	0.19732	0.19128	0.22	0.25291	0.27	RANDOM	14.113

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]
0.41			-0.22		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.64
r_dihedral_angle_4_deg	16.138
r_dihedral_angle_3_deg	14.314
r_dihedral_angle_1_deg	6.637
r_angle_other_deg	2.144
r_scangle_it	1.883
r_mcangle_it	1.776
r_scbond_it	1.685
r_mcbond_it	1.61
r_angle_refined_deg	1.271
r_nbd_other	0.212
r_mcbond_other	0.196
r_nbd_refined	0.189
r_nbtor_refined	0.188
r_symmetry_vdw_other	0.165
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.136
r_nbtor_other	0.082
r_chiral_restr	0.073
r_symmetry_vdw_refined	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002
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	4680
Nucleic Acid Atoms	505
Solvent Atoms	357
Heterogen Atoms	55

Software

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