1TUV

Crystal structure of YgiN in complex with menadione

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	sodium citrate, ammonium sulfate, sodium/potassium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.24	61.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.562	α = 90
b = 102.562	β = 90
c = 102.562	γ = 90

Symmetry
Space Group	P 41 3 2

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 210		2004-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9788	NSLS	X6A

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	1.69	50	100	0.07	0.07	50	8	19783	19783	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.69	1.77	99

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	direct input of native model	THROUGHOUT	1.7	25.65	19783	19783	1056	100	0.20949	0.20949	0.20756	0.24904	RANDOM	22.765

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
r_scangle_it	6.428
r_dihedral_angle_1_deg	6.102
r_scbond_it	4.137
r_mcangle_it	2.379
r_angle_refined_deg	2
r_mcbond_it	1.337
r_angle_other_deg	1.02
r_symmetry_vdw_other	0.4
r_symmetry_vdw_refined	0.284
r_nbd_other	0.261
r_nbd_refined	0.243
r_xyhbond_nbd_refined	0.235
r_symmetry_hbond_refined	0.223
r_chiral_restr	0.13
r_nbtor_other	0.092
r_bond_refined_d	0.024
r_gen_planes_other	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	797
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing