3L23

Crystal structure of Sugar phosphate isomerase/epimerase (YP_001303399.1) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	277	0.2000M MgAcetate, 20.0000% PEG-3350, No Buffer pH 7.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.657	α = 90
b = 56.634	β = 102.98
c = 78.188	γ = 90

Symmetry
Space Group	C 1 2 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)	2009-07-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97935	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	28.318	96.3	0.045	9.45	2.81		36149		-3	19.269

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	92.7		0.339	1.97

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	28.318	36149	1806	99.07	0.149	0.148	0.167	RANDOM	34.044

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]
-0.01		0.22	1.51		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.251
r_dihedral_angle_3_deg	12.562
r_dihedral_angle_4_deg	12.353
r_dihedral_angle_1_deg	5.299
r_scangle_it	3.062
r_scbond_it	2.375
r_angle_refined_deg	1.557
r_mcangle_it	1.385
r_mcbond_it	1.031
r_angle_other_deg	1.02
r_symmetry_hbond_refined	0.257
r_mcbond_other	0.255
r_symmetry_vdw_other	0.218
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.183
r_nbd_other	0.175
r_symmetry_vdw_refined	0.139
r_nbtor_other	0.088
r_chiral_restr	0.08
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_metal_ion_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2185
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction