3EJK | pdb_00003ejk

Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	30.0000% PEG-6000, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.79	α = 90
b = 86.51	β = 90
c = 51.34	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97911,0.97932	SSRL	BL9-2

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	1.95	29.722	98.5	0.102	7.09			13593		-3	17.509

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	1.95	2.02	96.9		0.497	1.7

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	1.95	29.722	13584	673	99.57	0.171	0.169	0.18	0.217	0.23	RANDOM	27.245

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]
0.66			-1.26		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.085
r_dihedral_angle_4_deg	12.499
r_dihedral_angle_3_deg	10.366
r_scangle_it	5.025
r_dihedral_angle_1_deg	3.84
r_scbond_it	3.374
r_mcangle_it	1.842
r_angle_refined_deg	1.721
r_angle_other_deg	1.413
r_mcbond_it	0.967

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.085
r_dihedral_angle_4_deg	12.499
r_dihedral_angle_3_deg	10.366
r_scangle_it	5.025
r_dihedral_angle_1_deg	3.84
r_scbond_it	3.374
r_mcangle_it	1.842
r_angle_refined_deg	1.721
r_angle_other_deg	1.413
r_mcbond_it	0.967
r_mcbond_other	0.177
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1211
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
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.