6GHS | pdb_00006ghs

Modification dependent TagI restriction endonuclease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CLZ	3clz, 5mkw
experimental model	PDB	5MKW	3clz, 5mkw

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	7.5	294	A5 Morpheus Buffer (10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5)

Crystal Properties
Matthews coefficient	Solvent content
4.4	72.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.963	α = 90
b = 72.963	β = 90
c = 207.576	γ = 90

Symmetry
Space Group	P 41 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	294	CCD	Bruker Platinum 135	HELIOS multilayer optics	2018-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.54

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	2.92	20	96.1	0.2386	0.2196	4.38	3.23		12496

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	2.92	3.02	96.2		0.6983	0.9485	1.2	3.3

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	3clz, 5mkw	2.92	20	11890	607	96.64	0.19389	0.19242	0.2	0.22309	0.23	RANDOM	51.062

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]
1.54			1.54		-3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.393
r_dihedral_angle_4_deg	21.054
r_dihedral_angle_3_deg	14.906
r_long_range_B_refined	7.486
r_long_range_B_other	7.481
r_dihedral_angle_1_deg	6.271
r_scangle_other	4.741
r_mcangle_it	4.623
r_mcangle_other	4.622
r_mcbond_it	2.689
r_mcbond_other	2.684
r_scbond_other	2.675
r_scbond_it	2.674
r_angle_refined_deg	1.338
r_angle_other_deg	0.932
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	2212
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data reduction
SAINT	data scaling
SADABS	data scaling
PHASER	phasing
FFFEAR	phasing
BALBES	phasing
BUCCANEER	model building
ARP/wARP	model building