2ODI | pdb_00002odi

Restriction Endonuclease BCNI-Cognate DNA Substrate Complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	294	0.02 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate pH 4.6 and 30% (v/v) 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.553	α = 90
b = 87.87	β = 90
c = 79.391	γ = 90

Symmetry
Space Group	P 21 21 2

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	BENT MIRROR	2006-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	0.97955	MPG/DESY, HAMBURG	BW6

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	1.45	30	97.8	0.05	8.5	3.7	99034	99034			12.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	96.3		0.25	2.9	3.7	14110

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.45	28.38	98979	98979	4977	97.5	0.175	0.175	0.174	0.18	0.199	0.2	RANDOM	13.875

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]
0.21			-0.06		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.596
r_dihedral_angle_4_deg	17.298
r_dihedral_angle_3_deg	11.937
r_dihedral_angle_1_deg	6.359
r_scangle_it	2.222
r_scbond_it	1.628
r_angle_refined_deg	1.192
r_mcangle_it	1.034
r_mcbond_it	0.971
r_nbtor_refined	0.302
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.193
r_symmetry_hbond_refined	0.157
r_metal_ion_refined	0.14
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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	3844
Nucleic Acid Atoms	890
Solvent Atoms	650
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SHELXD	phasing
SHARP	phasing
NCSREF	model building
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXE	model building
ARP/wARP	model building