4KYW | pdb_00004kyw

Restriction endonuclease DPNI in complex with two DNA molecules

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ESJ	PDB ENTRY 4ESJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	160 mM CALCIUM ACETATE, 80 mM SODIUM CACODYLATE PH 6.5, 14.4% W/V PEG 8000, 20% V/V GLYCEROL, 10 mM SPERMIDINE., VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.7	α = 90
b = 101.05	β = 90
c = 114.85	γ = 90

Symmetry
Space Group	C 2 2 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	PSI PILATUS 6M		2012-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	1.23953	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.35	50	99.7	0.049	0.049	20.51	6.37	23502	23502

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.41	99.9		0.44	0.44	4.14	6.68	1720

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 4ESJ	2.35	46.23	23477	23477	1204	99.72	0.20216	0.20216	0.20125	0.2	0.21904	0.21	RANDOM	43.385

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]
-0.77			-0.42		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.887
r_dihedral_angle_4_deg	19.589
r_dihedral_angle_3_deg	15.495
r_dihedral_angle_1_deg	6.217
r_angle_other_deg	3.804
r_scangle_it	2.848
r_scbond_it	1.794
r_angle_refined_deg	1.34
r_mcangle_it	1.282
r_mcbond_it	0.675
r_nbd_other	0.273
r_symmetry_vdw_other	0.222
r_metal_ion_refined	0.218
r_symmetry_hbond_refined	0.212
r_nbtor_refined	0.201
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.189
r_symmetry_vdw_refined	0.14
r_nbtor_other	0.109
r_chiral_restr	0.083
r_xyhbond_nbd_other	0.071
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_gen_planes_other	0.01
r_bond_other_d
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2096
Nucleic Acid Atoms	812
Solvent Atoms	94
Heterogen Atoms	3

Software

Software
Software Name	Purpose
MOLREP	phasing
ARP/wARP	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling