2F2H

Structure of the YicI thiosugar Michaelis complex

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	288	10 mg/ml protein, 100mM Na Acetate, pH 6.5, 2M Ammonium Sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.317	α = 90
b = 175.841	β = 90
c = 210.742	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	CCD	ADSC QUANTUM 4		2005-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.95516	ALS	8.2.2

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	1.95	28.64	86.5	0.097	0.097	7.3	3.4	375658	375731			16.6

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)
1	1.95	2.06	88.9		0.433	0.433	1.7	3	55875

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1XSI	1.95	28.64	375658	375658	18828	86.36	0.182	0.182	0.18	0.225	RANDOM	18.288

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]
-0.29			-1.31		1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.157
r_dihedral_angle_4_deg	19.024
r_dihedral_angle_3_deg	16.421
r_dihedral_angle_1_deg	7.565
r_scangle_it	3.068
r_scbond_it	2.163
r_angle_refined_deg	1.748
r_mcangle_it	1.33
r_mcbond_it	1.117
r_angle_other_deg	0.963
r_symmetry_vdw_other	0.282
r_mcbond_other	0.223
r_nbd_refined	0.205
r_nbd_other	0.199
r_symmetry_vdw_refined	0.199
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.125
r_nbtor_other	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37392
Nucleic Acid Atoms
Solvent Atoms	2003
Heterogen Atoms	404

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing