Experiment: 6UKF

HhaI endonuclease in Complex with DNA at 1 Angstrom Resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	292	35% v/v 2-propanol, 0.1 M sodium phosphate dibasic / citric acid, pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
1.98	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.018	α = 90
b = 37.317	β = 109.768
c = 69.027	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	PIXEL	DECTRIS EIGER X 16M		2019-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.8000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1	26.4	93.9	0.104	0.033	16.3	8.7		148223			10

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.01			1.069	0.588	0.378	0.9

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 6UKE	1	26.39	1.33	148028	1997	93.05	0.1549	0.1547	0.1553	0.1662	0.1654	19.14

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.9997
f_angle_d	0.8254
f_chiral_restr	0.0592
f_bond_d	0.0043
f_plane_restr	0.0041

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2077
Nucleic Acid Atoms	527
Solvent Atoms	258
Heterogen Atoms	74

Software

Software
Software Name	Purpose
SERGUI	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing