5MLO | pdb_00005mlo

Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 mM NaCl + 8% (v/v) DMSO + 31% pentaerythitol propoxylate (5/4 PO/OH)

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.136	α = 90
b = 86.802	β = 90
c = 156.679	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	PIXEL	DECTRIS PILATUS 6M-F		2016-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.1402	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.96	78.34	100	0.084	0.999	20.2	13		67566

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	2.01	100		1.763	0.566	1.5	13

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	1VYM	1.96	78.34	64155	3325	99.95	0.21363	0.21129	0.22	0.25933	0.26	RANDOM	44.945

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]
-0.27			-2.22		2.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.647
r_dihedral_angle_4_deg	16.818
r_dihedral_angle_3_deg	15.252
r_long_range_B_refined	8.498
r_long_range_B_other	8.404
r_dihedral_angle_1_deg	7.255
r_scangle_other	4.617
r_mcangle_it	3.904
r_mcangle_other	3.904
r_scbond_it	2.855
r_scbond_other	2.855
r_mcbond_it	2.452
r_mcbond_other	2.45
r_angle_refined_deg	1.401
r_angle_other_deg	1.091
r_chiral_restr	0.097
r_gen_planes_refined	0.012
r_bond_refined_d	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6175
Nucleic Acid Atoms
Solvent Atoms	385
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing