2IZO | pdb_00002izo

Structure of an Archaeal PCNA1-PCNA2-FEN1 Complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B43	PDB ENTRIES 1B43 FOR FEN1 AND 1VYJ FOR PCNA1 AND PCNA2
experimental model	PDB	1VYJ	PDB ENTRIES 1B43 FOR FEN1 AND 1VYJ FOR PCNA1 AND PCNA2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			PRIOR TO CRYSTALLISATION THE PCNA1-PCNA2-PCNA3 COMPLEX WAS MIXED WITH FEN1 AT AN EQUIMOLAR RATIO AND INCUBATED FOR 20 MIN AT 294 K. PCNA1-PCNA2-FEN1 CO-CRYSTALS WERE GROWN BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS. PCNA3 WAS NOT PRESENT IN THE CRYSTAL LATTICE. DROPS WERE PREPARED BY MIXING 100 MM PROTEIN COMPLEX IN 20 MM TRIS-HCL PH 8.0, 200 MM NACL, 5 MM MGCL2, 2 MM DTT BUFFER SOLUTION WITH EQUAL VOLUMES OF 0.1M ACETATE PH 4.8, 8% PEG 8,000, 220 MM ZNOAC2 AND 30 MM GLYCYL-GLYCYL-GLYCINE.

Crystal Properties
Matthews coefficient	Solvent content
2.45	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.986	α = 90
b = 99.774	β = 90
c = 99.958	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 CCD		2005-09-07	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)	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	2.8	60	99.3	0.08	15.3	4.8		23534			71.32

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	2.8	2.95	99.8		0.57	3	4.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1B43 FOR FEN1 AND 1VYJ FOR PCNA1 AND PCNA2	2.9	30	20108	1088	98.9	0.253	0.25	0.25	0.312	0.31	RANDOM	49.71

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]
0.55			-4.11		3.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.938
r_dihedral_angle_3_deg	17.26
r_dihedral_angle_4_deg	16.199
r_dihedral_angle_1_deg	5.27
r_angle_refined_deg	1.031
r_scangle_it	0.746
r_scbond_it	0.436
r_symmetry_hbond_refined	0.387
r_mcangle_it	0.319
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.197
r_mcbond_it	0.185
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5725
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing