3IMB | pdb_00003imb

Alternative binding mode of restriction endonuclease BcnI to cognate DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ODI	PDB ENTRY 2odi

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	294	0.16M Ammonium Sulfate, 0.08M Sodium Acetate trihydrate pH 4.6, 20% w/v Polyethylene Glycol 4000, 20% v/v Glycerol Anhydrous, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.562	α = 90
b = 84.053	β = 100.09
c = 98.947	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH	BENT MIRROR	2006-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	1.89	20	98.4	0.089	0.089	5.4	2.3	98933	98933			18.8

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)
	1.89	2	99.6		0.236	0.236	3.1	2.3	14591

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 (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 2odi	1.89	19.81	98906	98906	4977	98.19	0.21405	0.21211	0.22	0.25101	0.25	RANDOM	20.1847

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]
0.39		-0.02	0.1		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.282
r_dihedral_angle_4_deg	16.135
r_dihedral_angle_3_deg	13.634
r_dihedral_angle_1_deg	6.964
r_angle_other_deg	3.973
r_scangle_it	2.19
r_scbond_it	1.558
r_angle_refined_deg	1.263
r_mcangle_it	0.973
r_mcbond_it	0.579
r_nbd_other	0.247
r_symmetry_vdw_refined	0.231
r_symmetry_vdw_other	0.213
r_nbtor_refined	0.186
r_nbd_refined	0.184
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.143
r_nbtor_other	0.107
r_chiral_restr	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.007
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
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	7688
Nucleic Acid Atoms	1452
Solvent Atoms	729
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling