5ZUT

Crystal Structure of Yeast PCNA in Complex with N24 Peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6B8I	6B8I, 5DA7
experimental model	PDB	5DA7	6B8I, 5DA7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	n-Octyl-b-D-glu, NaCi pH 5.5, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.82	61.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.35	α = 90
b = 84.03	β = 93.62
c = 58.15	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	PIXEL	DECTRIS EIGER X 16M		2018-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

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	2.83	58.03	98.7	0.133		6.9		9212

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	2.83	2.9	99.4		0.512		7.2

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	6B8I, 5DA7	2.82	58.03	8684	527	98.4	0.3301	0.326	0.3966	RANDOM	99.825

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]
67.58		114.5	-81.24		13.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.033
r_dihedral_angle_4_deg	22.145
r_dihedral_angle_3_deg	20.118
r_dihedral_angle_1_deg	8.837
r_mcangle_it	5.734
r_mcbond_it	3.493
r_mcbond_other	3.49
r_angle_other_deg	1.392
r_angle_refined_deg	1.063
r_chiral_restr	0.043
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2155
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling