2OBC

The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M MES pH 6.5, 3% (v/v) 1,6 Hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.1	α = 90
b = 173.1	β = 90
c = 76.7	γ = 120

Symmetry
Space Group	P 31 2 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	ADSC QUANTUM 4		2004-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3	30	99.8	0.081	0.081	17.2	4.9	26730	26665	-3	-3	59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.1	99.1		0.409	0.409	3.8	4.8	2435

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2G6V	3	28.86	26665	25319	1346	99.9	0.22502	0.22502	0.22227	0.27557	RANDOM	58.742

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]
-0.33	-0.17		-0.33		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.888
r_dihedral_angle_3_deg	20.43
r_dihedral_angle_4_deg	18.179
r_dihedral_angle_1_deg	6.877
r_scangle_it	1.837
r_angle_refined_deg	1.345
r_scbond_it	1.064
r_mcangle_it	0.847
r_mcbond_it	0.503
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.888
r_dihedral_angle_3_deg	20.43
r_dihedral_angle_4_deg	18.179
r_dihedral_angle_1_deg	6.877
r_scangle_it	1.837
r_angle_refined_deg	1.345
r_scbond_it	1.064
r_mcangle_it	0.847
r_mcbond_it	0.503
r_nbtor_refined	0.305
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.207
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5472
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	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 R01GM133198.