1R6Y

Crystal structure of YgiN from Escherichia coli

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	Ammonium Sulphate, Tri-Sodium Citrate, Sodium/Potassium Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.057	α = 90
b = 102.057	β = 90
c = 102.057	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 4		2002-04-25	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH		2003-04-11	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	1.199998	CHESS	F1
2	SYNCHROTRON	NSLS BEAMLINE X9A	0.979383, 0.979228, 0.971708	NSLS	X9A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	50	99.7			9700	9700	2	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.2	2.28	99.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MAD	THROUGHOUT	2.2	19.65	2	9700	9700	467	100	0.21031	0.21031	0.20842	0.24948	RANDOM	37.566

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	7.551
r_dihedral_angle_1_deg	6.951
r_scbond_it	4.66
r_mcangle_it	3.012
r_angle_refined_deg	2.33
r_mcbond_it	1.666
r_angle_other_deg	1.037
r_symmetry_vdw_other	0.445
r_symmetry_vdw_refined	0.284
r_nbd_refined	0.269
r_nbd_other	0.256
r_xyhbond_nbd_refined	0.213
r_chiral_restr	0.153
r_nbtor_other	0.102
r_symmetry_hbond_refined	0.062
r_bond_refined_d	0.04
r_gen_planes_refined	0.012
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	797
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing