2EX3 | pdb_00002ex3

Bacteriophage phi29 DNA polymerase bound to terminal protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		A lower resolution partially refined complex determined by heavy atom phasing

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	Polymerase (6.7 mg/ml), terminal protein (3.3 mg/ml) in 50 mM NaCl, 50 mM Tris-HCl pH 7.5, 20 mM Ammonium sulfate, 1 mM dithiothreitol, mixed with an equal volume of well solution containing: 2.0 M sodium/potassium phosphate, pH 7, 100 mM sodium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.86	74.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 304.933	α = 90
b = 220.281	β = 45.4
c = 217.165	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	Monochromator	2004-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	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	3	50	99.9	0.085		3.8	202498	202295		-3

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	3	3.11	100		0.01	1.25	3.8	20192

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	A lower resolution partially refined complex determined by heavy atom phasing	3	48.85	182124	202285	20161	99.68	0.203	0.203	0.2	0.2	0.229	0.23	RANDOM	99.908

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]
-0.5		0.51	0.08		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.37
r_dihedral_angle_3_deg	16.951
r_dihedral_angle_4_deg	15.145
r_scangle_it	7.498
r_dihedral_angle_1_deg	5.166
r_scbond_it	4.723
r_mcangle_it	2.81
r_mcbond_it	1.61
r_angle_refined_deg	1.002
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.37
r_dihedral_angle_3_deg	16.951
r_dihedral_angle_4_deg	15.145
r_scangle_it	7.498
r_dihedral_angle_1_deg	5.166
r_scbond_it	4.723
r_mcangle_it	2.81
r_mcbond_it	1.61
r_angle_refined_deg	1.002
r_nbtor_refined	0.307
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.131
r_symmetry_vdw_refined	0.128
r_symmetry_hbond_refined	0.077
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37092
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	16

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.