5TH3 | pdb_00005th3

Restriction/modification system-Type II R.SwaI cleaved DNA complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SwaI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	24-28% PEG1000, 100 mM TrisHCl, 5 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.28	48.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.748	α = 90
b = 57.072	β = 107.6
c = 113.443	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	RIGAKU SATURN 70		2014-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5400

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	2.33	50	98.2	9.5	17.8	7.1		56787		1	33.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.33	2.41	85.9		0.984	0.678	1.35	4.7

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	SwaI	2.33	50.01	53845	2894	98.15	0.20051	0.19846	0.2	0.23891	0.23	RANDOM	75.98

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]
-1.39		-0.64	4.16		-1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.169
r_dihedral_angle_4_deg	19.285
r_dihedral_angle_3_deg	17.29
r_long_range_B_refined	7.145
r_long_range_B_other	7.145
r_dihedral_angle_1_deg	6.83
r_scangle_other	5.007
r_mcangle_it	3.745
r_mcangle_other	3.744
r_scbond_it	3.308
r_scbond_other	3.308
r_mcbond_it	2.418
r_mcbond_other	2.41
r_angle_refined_deg	2.127
r_angle_other_deg	1.746
r_chiral_restr	0.115
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.01
r_gen_planes_other	0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7576
Nucleic Acid Atoms	2127
Solvent Atoms	133
Heterogen Atoms	22

Software

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