Experiment: 5GKK

Crystal structure of a homing endonuclease, I-TnaI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BP7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	294	100 mM Hepes, 35% Jeffamine ED-2001

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.203	α = 90
b = 113.886	β = 110.41
c = 44.922	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	ADSC QUANTUM 315r		2011-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.54175	SSRF	BL17U

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	50	96.5	0.086	16.4	6.2		19699			37.3

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	2	2.07	96		0.719	4.3	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1BP7	2.001	39.49	1.37	19667	995	96.16	0.2071	0.2047	0.1985	0.2479	0.2367	Random	46.5213

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]
-2.7089		-3.3439	10.0693		-7.3604

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.438
f_angle_d	1.275
f_chiral_restr	0.096
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2450
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data processing
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement