2PZS | pdb_00002pzs

Phi29 DNA polymerase complexed with primer-template DNA (post-translocation binary 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 358-394

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	100 mM Tris-HCl, 20% PEG 10000, 200 mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 216.633	α = 90
b = 146.292	β = 117.93
c = 115.054	γ = 90

Symmetry
Space Group	C 1 2 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		2005-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.10000	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	50	98.4	0.152	5.8	2.1	97325	95762		-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)
	2.6	2.69	95.1		0.773	1	2.1

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 (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 358-394	2.6	45.22	97325	85919	9703	98.32	0.22452	0.21872	0.24	0.27524	0.29	RANDOM	22.349

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]
0.15		0.26	0.01		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.875
r_dihedral_angle_3_deg	17.311
r_dihedral_angle_4_deg	16.026
r_dihedral_angle_1_deg	6.778
r_scangle_it	1.894
r_mcangle_it	1.491
r_scbond_it	1.344
r_angle_refined_deg	1.239
r_mcbond_it	1.188
r_angle_other_deg	0.87
r_symmetry_vdw_refined	0.294
r_symmetry_hbond_refined	0.287
r_symmetry_vdw_other	0.232
r_mcbond_other	0.221
r_nbd_refined	0.207
r_nbtor_refined	0.193
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.083
r_nbtor_other	0.083
r_xyhbond_nbd_other	0.046
r_bond_refined_d	0.011
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	18487
Nucleic Acid Atoms	1207
Solvent Atoms	89
Heterogen Atoms

Software

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