3I7D

Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi (YP_168127.1) from SILICIBACTER POMEROYI DSS-3 at 2.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.33	277	24.0000% polyethylene glycol 8000, 0.3000M sodium acetate, 0.1M sodium cacodylate pH 6.33, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.815	α = 90
b = 52.815	β = 90
c = 252.163	γ = 90

Symmetry
Space Group	P 41 21 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	2009-01-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97959,0.97941	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	2.3	29.761	99.9	0.336	0.336	8.3	9.3		16869			23.149

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	2.3	2.36	99.7		0.012	1.204	0.6	9.5	1188

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	2.3	29.761	16826	850	99.75	0.198	0.196	0.245	RANDOM	32.484

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]
0.4			0.4		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.215
r_dihedral_angle_3_deg	14.248
r_dihedral_angle_4_deg	12.146
r_dihedral_angle_1_deg	6.168
r_scangle_it	4.001
r_scbond_it	3.1
r_mcangle_it	2.081
r_mcbond_it	1.644
r_angle_refined_deg	1.369
r_angle_other_deg	0.886
r_mcbond_other	0.357
r_symmetry_vdw_other	0.311
r_symmetry_hbond_refined	0.224
r_nbd_other	0.201
r_nbd_refined	0.195
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.164
r_symmetry_vdw_refined	0.108
r_nbtor_other	0.085
r_chiral_restr	0.076
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2378
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing