3SC6

2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	297	Protein: 7.5 mg/mL in buffer containing 10 mM Tris HCl pH 8.3, 500 mM NaCl, and 5 mM BME, 5 mM MgCl2, 1 mM NADP+, and 10% glycerol.Crystallization conditions: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, and 25% w/v PEG 5000 MME

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.449	α = 90
b = 113.337	β = 91.18
c = 144.949	γ = 90

Symmetry
Space Group	P 1 21 1

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 300 mm CCD	Mirror	2011-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97856	APS	21-ID-D

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	2.65	30	100	0.102	11.49	3.8	75200	75200		-3	67.1

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	2.65	2.7	100		0.615	2.35	3.8	3724

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1VL0	2.65	29.9	70861	70861	3745	99.94	0.21747	0.21531	0.25785	RANDOM	56.691

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]
4.94		0.53	-0.35		-4.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	9.937
r_dihedral_angle_4_deg	4.542
r_dihedral_angle_3_deg	4.01
r_scangle_it	3.011
r_scbond_it	1.822
r_angle_refined_deg	1.359
r_mcangle_it	1.172
r_angle_other_deg	0.791
r_dihedral_angle_1_deg	0.68
r_mcbond_it	0.606

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	9.937
r_dihedral_angle_4_deg	4.542
r_dihedral_angle_3_deg	4.01
r_scangle_it	3.011
r_scbond_it	1.822
r_angle_refined_deg	1.359
r_mcangle_it	1.172
r_angle_other_deg	0.791
r_dihedral_angle_1_deg	0.68
r_mcbond_it	0.606
r_mcbond_other	0.103
r_chiral_restr	0.083
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13571
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	373

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.