3RYK | pdb_00003ryk

1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) from Bacillus anthracis str. Ames with TDP and PPi bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DZR	PDB ENTRY 1DZR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	Protein: 7.5 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: The JCSG+ suite (condition A3(#3): 0.2 M di-Ammonium citrate pH 5.0, 20 % w/v PEG3350). Crystallized at 1:1 v/v ratio. Cryo: soak in The JCSG+ A3. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.652	α = 90
b = 86.652	β = 90
c = 45.101	γ = 120

Symmetry
Space Group	P 3

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	2011-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97919	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	1.63	30	99.9	0.052	26.53	4.8	47039	47039		-3	24.6

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	1.63	1.66	98.5		0.488	2.87	4.4	2273

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DZR	1.631	28.85	44611	44611	2425	99.75	0.12476	0.12299	0.13	0.16006	0.17	RANDOM	21.231

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]
-19.55			-19.55		39.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.879
r_dihedral_angle_3_deg	5.831
r_dihedral_angle_4_deg	5.375
r_scangle_it	4.441
r_scbond_it	3.093
r_mcangle_it	1.897
r_angle_refined_deg	1.852
r_dihedral_angle_1_deg	1.427
r_rigid_bond_restr	1.252
r_mcbond_it	1.248

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.879
r_dihedral_angle_3_deg	5.831
r_dihedral_angle_4_deg	5.375
r_scangle_it	4.441
r_scbond_it	3.093
r_mcangle_it	1.897
r_angle_refined_deg	1.852
r_dihedral_angle_1_deg	1.427
r_rigid_bond_restr	1.252
r_mcbond_it	1.248
r_angle_other_deg	0.98
r_mcbond_other	0.472
r_chiral_restr	0.109
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2814
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	34

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 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.