2ZVM

Crystal structure of PCNA in complex with DNA polymerase iota fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VYM	PDB ENTRY 1VYM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	HANGING DROP VAPOR DIFFUSION	6.4	293	pH6.4, HANGING DROP VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.62	α = 90
b = 68.82	β = 95.05
c = 90.18	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 210	Rhodium coated silicon single crystal mirrors	2007-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1	Photon Factory	AR-NW12A

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	2.3	50	98	0.067	13.5	4.1		44815		-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)
1	2.3	2.38	86.4		0.338	3.2	3	4440

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1VYM	2.3	19.95	42715	2249	100	0.19627	0.19335	0.2512	RANDOM	42.506

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]
-0.53		0.43	0.4		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.167
r_dihedral_angle_4_deg	19.853
r_dihedral_angle_3_deg	16.58
r_dihedral_angle_1_deg	7.385
r_angle_other_deg	4.42
r_scangle_it	4.241
r_scbond_it	2.841
r_angle_refined_deg	1.79
r_mcangle_it	1.78
r_mcbond_it	1.533
r_symmetry_vdw_other	0.385
r_symmetry_hbond_refined	0.242
r_nbd_other	0.241
r_symmetry_vdw_refined	0.24
r_nbd_refined	0.211
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.173
r_nbtor_other	0.118
r_chiral_restr	0.105
r_mcbond_other	0.027
r_bond_refined_d	0.02
r_gen_planes_other	0.009
r_gen_planes_refined	0.006
r_bond_other_d
r_xyhbond_nbd_other
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	5985
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing