7WP3 | pdb_00007wp3

Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from Leishmania donovani with 1,5-Bis (4-amidinophenoxy) pentane (PNT) at 2.95 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5B7O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	20% PEG 3350, 200mM sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.024	α = 90
b = 150.664	β = 90
c = 170.547	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	MARRESEARCH		2015-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.95	43.49	98.8	0.12	11.6	4.9		72691

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	2.95	3.03	84.52		0.49	1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5B7O	2.954	43.485	72691	1437	98.807	0.212	0.211	0.21	0.2567	0.25	90.593

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]
0.136			0.044		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.76
r_lrange_it	19.41
r_lrange_other	19.41
r_scangle_it	14.274
r_scangle_other	14.274
r_dihedral_angle_3_deg	12.375
r_mcangle_it	11.062
r_mcangle_other	11.062
r_dihedral_angle_4_deg	10.342
r_scbond_it	9.336
r_scbond_other	9.33
r_mcbond_other	7.425
r_mcbond_it	7.424
r_dihedral_angle_1_deg	5.864
r_angle_other_deg	2.291
r_dihedral_angle_other_2_deg	1.815
r_angle_refined_deg	1.31
r_nbd_other	0.505
r_symmetry_nbd_refined	0.468
r_symmetry_xyhbond_nbd_refined	0.359
r_symmetry_nbd_other	0.231
r_nbd_refined	0.218
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_other	0.078
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.05
r_bond_other_d	0.035
r_bond_refined_d	0.007
r_gen_planes_other	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11514
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	50

Software

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