4Z1X | pdb_00004z1x

Crystal structure of LAGLIDADG homing endonuclease I-GzeII in complex with DNA target

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QQY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	30% PEG 6000 0.1M HEPES pH 7.5 2mM CaCl2 26bp duplex DNA with single base 3' overhang

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.833	α = 90
b = 61.186	β = 116.3
c = 128.871	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315r		2011-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.999	ALS	5.0.2

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	2.8	115.526	98.7	0.091	22.9	6.5		20664

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)
	2.8	2.9	90		0.34	2.8	4.1

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	3QQY	2.8	50	20664	1113	98.66	0.1764	0.173	0.18	0.2402	0.24	RANDOM	41.118

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]
1.65		-2.21	2.15		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.305
r_dihedral_angle_3_deg	18.1
r_dihedral_angle_4_deg	16.862
r_dihedral_angle_1_deg	6.273
r_mcangle_it	2.877
r_mcbond_it	1.657
r_mcbond_other	1.652
r_angle_refined_deg	1.517
r_angle_other_deg	1.298
r_chiral_restr	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4603
Nucleic Acid Atoms	2170
Solvent Atoms	129
Heterogen Atoms	4

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building