7PWH

Structure of the dTDP-sugar epimerase StrM

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	10% PEG 6000, 30% PEG 300, 100 mM CaCl2, 50 mM Tris pH 7.0 + 10 mM dTDP

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.376	α = 90
b = 131.542	β = 90
c = 78.539	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		2019-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	1.9	50.42	99.4	0.991	5.5	4.3		17624

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	1.9	1.94			0.312

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4HMZ	1.9	50.42	17601	925	99.138	0.203	0.2009	0.2495	28.068

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]
-1.435			0.191		1.244

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.323
r_dihedral_angle_4_deg	16.852
r_dihedral_angle_3_deg	15.799
r_lrange_it	8.382
r_dihedral_angle_1_deg	6.567
r_scangle_it	4.45
r_mcangle_it	3.636
r_scbond_it	2.878
r_mcbond_it	2.272
r_angle_refined_deg	1.401

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.323
r_dihedral_angle_4_deg	16.852
r_dihedral_angle_3_deg	15.799
r_lrange_it	8.382
r_dihedral_angle_1_deg	6.567
r_scangle_it	4.45
r_mcangle_it	3.636
r_scbond_it	2.878
r_mcbond_it	2.272
r_angle_refined_deg	1.401
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.219
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.15
r_chiral_restr	0.107
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1567
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	42

Software

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

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 R01GM133198.