7PWB | pdb_00007pwb

dTDP-sugar epimerase from Coxiella burnetii in complex with dTDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IXI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	7% PEG 4000 (w/v), 30% PEG 400, 5% dTDP (v/v), 29 mM citrate buffer pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.882	α = 90
b = 82.151	β = 90
c = 163.831	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	PIXEL	DECTRIS PILATUS 6M		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.87	81.915	84.8	0.998	12.5	6.6		37452

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.995	25		0.67

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2IXI	1.87	81.915	37452	1856	84.439	0.21	0.209	0.21	0.2366	0.24	40.645

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]
0.05			0.008		-0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.034
r_dihedral_angle_4_deg	18.259
r_dihedral_angle_3_deg	16.799
r_lrange_it	8.622
r_lrange_other	8.62
r_dihedral_angle_1_deg	7.615
r_scangle_it	6.383
r_scangle_other	6.382
r_mcangle_it	4.729
r_mcangle_other	4.696
r_scbond_it	4.2
r_scbond_other	4.199
r_mcbond_it	3.535
r_mcbond_other	3.498
r_angle_refined_deg	1.588
r_angle_other_deg	1.287
r_nbd_other	0.288
r_symmetry_nbd_refined	0.265
r_symmetry_xyhbond_nbd_refined	0.218
r_nbd_refined	0.203
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_other	0.111
r_ncsr_local_group_1	0.097
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.083
r_xyhbond_nbd_other	0.051
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3120
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
autoPROC	data scaling
autoPROC	data processing
Coot	model building
STARANISO	data scaling
MoRDa	phasing