6T22 | pdb_00006t22

N-terminal domain of EcoKMcrA restriction endonuclease (NEco) in complex with T5hmCGA target sequence

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GHC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	1.8 ul of protein-DNA solution (436:523 uM) was mixed with 2.2 ul of the F1 condition of the PACT premier crystal screen (MDL) (0.2 M Sodium fluoride, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG 3350) and cryo-protected with an addition of 25% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.417	α = 90
b = 113.417	β = 90
c = 156.367	γ = 120

Symmetry
Space Group	P 61 2 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	PIXEL	DECTRIS EIGER X 16M		2019-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9195	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.21	33.54	99.2	0.084	0.086	1	38.15	35.8		30298			55.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.34	95.4		1.761	1.802	0.734	1.91	20.8

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	6GHC	2.21	33.54	28708	1534	99.21	0.1592	0.157	0.16	0.2034	0.21	RANDOM	53.522

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]
-0.31	-0.16		-0.31		1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.341
r_dihedral_angle_4_deg	13.773
r_dihedral_angle_3_deg	12.54
r_dihedral_angle_1_deg	6.284
r_angle_other_deg	1.294
r_angle_refined_deg	1.21
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.341
r_dihedral_angle_4_deg	13.773
r_dihedral_angle_3_deg	12.54
r_dihedral_angle_1_deg	6.284
r_angle_other_deg	1.294
r_angle_refined_deg	1.21
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2320
Nucleic Acid Atoms	816
Solvent Atoms	405
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.