2ZVL | pdb_00002zvl

Crystal structure of PCNA in complex with DNA polymerase kappa 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	5.2	293	pH5.2, HANGING DROP VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.769	α = 87.25
b = 74.707	β = 77.46
c = 109.049	γ = 80.26

Symmetry
Space Group	P 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	RIGAKU MSC JUPITER 210	mirrors	2006-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1	SPring-8	BL38B1

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	2.5	50	90.6	0.082	9.1	2.7		71006		-3	53

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	2.5	2.59	90.6		0.241	4.1	2.3

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 ENTRY 1VYM	2.5	20	67254	3575	100	0.22865	0.22542	0.22	0.28943	0.28	RANDOM	37.715

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]
-1.04	-0.1	0.45	-0.12	0.19	0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.488
r_dihedral_angle_4_deg	19.537
r_dihedral_angle_3_deg	19.307
r_dihedral_angle_1_deg	6.9
r_scangle_it	5.402
r_scbond_it	3.484
r_mcangle_it	2.305
r_angle_refined_deg	1.872
r_mcbond_it	1.317
r_angle_other_deg	1.235
r_mcbond_other	0.349
r_chiral_restr	0.101
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11928
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing