3F2B | pdb_00003f2b

DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.3	289	20% PEG 2000 MME, 0.1M PHOSPHATE- CITRATE, 200MM LITHIUM SULFATE, PH 5.3, VAPOR DIFFUSION, pH 5.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.174	α = 90
b = 140.793	β = 90
c = 184.524	γ = 90

Symmetry
Space Group	C 2 2 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			2008-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.999887	ALS	5.0.1

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	2.4	43.52	99.9	0.101	10.2	5.8		59793

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	2.4	2.49	100		0.824		4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	2.39	43.52	59703	3017		0.231	0.228	0.23	0.273	0.27	RANDOM	43.59

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]
-1.77			2.29		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.326
r_dihedral_angle_4_deg	20.495
r_dihedral_angle_3_deg	20.471
r_dihedral_angle_1_deg	6.088
r_scangle_it	2.553
r_angle_refined_deg	1.609
r_scbond_it	1.593
r_mcangle_it	0.981
r_mcbond_it	0.512
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.326
r_dihedral_angle_4_deg	20.495
r_dihedral_angle_3_deg	20.471
r_dihedral_angle_1_deg	6.088
r_scangle_it	2.553
r_angle_refined_deg	1.609
r_scbond_it	1.593
r_mcangle_it	0.981
r_mcbond_it	0.512
r_chiral_restr	0.108
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7815
Nucleic Acid Atoms	631
Solvent Atoms	95
Heterogen Atoms	50

Software

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

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.