4AAD | pdb_00004aad

Crystal structure of the mutant D75N I-CreI in complex with its wild- type target in absence of metal ions at the active site (The four central bases, 2NN region, are composed by GTAC from 5' to 3')

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XE0	PDB ENTRY 2XE0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		20% PEG300, 0.1M TRIS PH 8.5, 5% PEG8000, 10% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
3.36	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.406	α = 90
b = 84.668	β = 90
c = 159.959	γ = 90

Symmetry
Space Group	P 2 21 21

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 PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS		SLS

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.1	47.44	99.9	0.05	7.9	4.3		12755		2	86.59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.27	100		0.31	2.5	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2XE0	3.1	47.206	1.34	12750	1276	99.79	0.2126	0.2097	0.21	0.2378	0.24

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]
-4.0402			1.6569		2.3833

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	25.079
f_angle_d	1.036
f_chiral_restr	0.063
f_bond_d	0.004
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2464
Nucleic Acid Atoms	978
Solvent Atoms	26
Heterogen Atoms	48

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

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.