3OBE

Crystal structure of a sugar phosphate isomerase/epimerase (BDI_3400) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.56	277	5.0% polyethylene glycol 1000, 32.9% Ethanol, 0.1M phosphate-citrate pH 4.56, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.745	α = 77.8
b = 48.69	β = 74.67
c = 79.88	γ = 68.9

Symmetry
Space Group	P 1

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 mirror (vertical focusing)	2009-12-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97910	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.7	27.437	87.3	0.045	10.89			64918		-3	17.188

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	80.8		0.252	2.2	1.99

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.7	27.437	64915	3301	96.24	0.141	0.1398	0.1637	RANDOM	24.0093

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]
0.72	-0.26	-0.5	-0.25	0.52	-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.235
r_dihedral_angle_4_deg	16.836
r_dihedral_angle_3_deg	13.136
r_dihedral_angle_1_deg	6.416
r_scangle_it	3.8
r_scbond_it	2.43
r_angle_refined_deg	1.612
r_mcangle_it	1.611
r_angle_other_deg	1.229
r_mcbond_it	0.931

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.235
r_dihedral_angle_4_deg	16.836
r_dihedral_angle_3_deg	13.136
r_dihedral_angle_1_deg	6.416
r_scangle_it	3.8
r_scbond_it	2.43
r_angle_refined_deg	1.612
r_mcangle_it	1.611
r_angle_other_deg	1.229
r_mcbond_it	0.931
r_mcbond_other	0.284
r_chiral_restr	0.097
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4589
Nucleic Acid Atoms
Solvent Atoms	574
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

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.