3FLO | pdb_00003flo

Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.411	α = 90
b = 142.633	β = 102.33
c = 175.255	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 Q315R	silicon monochromator	2007-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	31.9	99.8	0.102	0.102	5.2	7.3	141597	141597			58.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	99.7		0.652	0.652	1.2	7.4	20778

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	2.5	31.9	134185	7082	99.8	0.192	0.191	0.21	0.218	0.24	RANDOM	43.61

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]
0.51		-0.45	-0.8		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.132
r_dihedral_angle_4_deg	20.359
r_dihedral_angle_3_deg	15.726
r_dihedral_angle_1_deg	6.323
r_scangle_it	2.746
r_scbond_it	2.056
r_angle_refined_deg	1.545
r_mcangle_it	1.154
r_mcbond_it	0.997
r_angle_other_deg	0.976
r_nbd_refined	0.21
r_symmetry_vdw_other	0.209
r_nbd_other	0.199
r_symmetry_hbond_refined	0.198
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_other	0.152
r_mcbond_other	0.136
r_symmetry_vdw_refined	0.127
r_chiral_restr	0.09
r_nbtor_other	0.09
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002
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	19648
Nucleic Acid Atoms
Solvent Atoms	571
Heterogen Atoms	333

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing