3QC0

Crystal structure of a sugar isomerase (SMc04130) from SINORHIZOBIUM MELILOTI 1021 at 1.45 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	50.0% PEG-200, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.796	α = 90
b = 70.796	β = 90
c = 264.721	γ = 120

Symmetry
Space Group	P 61 2 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	MARMOSAIC 325 mm CCD	FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR	2010-03-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97929,0.97915	SSRL	BL9-2

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	1.45	29.865	100	0.075	0.075	11.2	5.8	70842	70842			16.06

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	1.45	1.49	99.8		0.692	0.692	2.3	5.8	5109

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.45	29.865	70726	3571	99.94	0.1607	0.1594	0.17	0.1846	0.2	RANDOM	24.3082

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]
2.09	1.04		2.09		-3.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.143
r_dihedral_angle_4_deg	17.581
r_dihedral_angle_3_deg	11.886
r_sphericity_free	10.728
r_sphericity_bonded	6.336
r_dihedral_angle_1_deg	6.332
r_scangle_it	4.701
r_scbond_it	3.189
r_mcangle_it	2.223
r_angle_refined_deg	1.835

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2041
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	101

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	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.