7PWI | pdb_00007pwi

Structure of the dTDP-sugar epimerase StrM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HMZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	10% PEG 6,000, 30% PEG 300, 100 mM CaCl2, 50 mM Tris pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.349	α = 90
b = 132.361	β = 90
c = 77.557	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		2018-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.326	66.18	74	0.996	10	6.3		36601

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	1.326	1.433	20.8		0.304

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	4HMZ	1.326	66.18	36601	1849	71.823	0.201	0.1996	0.2	0.2344	0.23	15.358

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]
-0.186			0.232		-0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.322
r_dihedral_angle_4_deg	21.655
r_dihedral_angle_3_deg	13.875
r_lrange_it	7.802
r_scangle_it	7.628
r_dihedral_angle_1_deg	5.907
r_scbond_it	5.639
r_mcangle_it	3.638
r_mcbond_it	3.587
r_angle_refined_deg	1.777

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.322
r_dihedral_angle_4_deg	21.655
r_dihedral_angle_3_deg	13.875
r_lrange_it	7.802
r_scangle_it	7.628
r_dihedral_angle_1_deg	5.907
r_scbond_it	5.639
r_mcangle_it	3.638
r_mcbond_it	3.587
r_angle_refined_deg	1.777
r_nbtor_refined	0.315
r_nbd_refined	0.214
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_refined	0.165
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.13
r_gen_planes_refined	0.012
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1546
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
STARANISO	data scaling
MoRDa	phasing

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.