1KCF

Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	4.6	287	Ammonium Sulphate, Sodium acetate, pH 4.6, microbatch, temperature 287K
2	MICROBATCH	8.5	287	Dihydrogen Phosphate, Tris-Hcl, pH 8.5, microbatch, temperature 287K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72	α = 90
b = 133.94	β = 90
c = 73.25	γ = 90

Symmetry
Space Group	P 21 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	IMAGE PLATE	MARRESEARCH	Mirrors	2001-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.93400	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	29.34	91.9	0.04	0.034	16	3.6	35212	31239	2	2	43.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.42	90.5		0.2	0.17	3.6	3.2	4787

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Single Wavelength Anomalous Dispersion	THROUGHOUT	2.3	29.34	31239	31239	1518	95	0.242	0.242	0.238	0.27	RANDOM	55.7

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]
13.7			-7.53		-6.17

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.1
c_scangle_it	3.63
c_mcangle_it	2.79
c_scbond_it	2.68
c_mcbond_it	1.65
c_angle_deg	1
c_improper_angle_d	0.65
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3738
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SOLVE	phasing
RESOLVE	model building
CNS	refinement
DENZO	data reduction
CCP4	data scaling
RESOLVE	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.