2Q1T | pdb_00002q1t

Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BXK	PDB ENTRIES 1BXK, 1KEU, 1R6D
experimental model	PDB	1KEU	PDB ENTRIES 1BXK, 1KEU, 1R6D
experimental model	PDB	1R6D	PDB ENTRIES 1BXK, 1KEU, 1R6D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	0.1 M bicine, 16 % (w/w) PEG 8000. UDP was added by soaking prior to cryo-protection., pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.442	α = 90
b = 78.119	β = 108.08
c = 59.262	γ = 90

Symmetry
Space Group	C 1 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 315		2006-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.977	ESRF	ID14-4

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	1.75	50	93.3	0.049	23.7	3.9	36325	33895		2	25.8

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	1.75	1.78	62.6		0.337	2.38	2.4	1137

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1BXK, 1KEU, 1R6D	1.75	28.52	36325	33887	1677	93.23	0.183	0.18302	0.183	0.18	0.219	RANDOM	40.4

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]
0.01		-1.1	1.55		-2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.575
r_dihedral_angle_4_deg	22.06
r_dihedral_angle_3_deg	14.653
r_dihedral_angle_1_deg	14.078
r_scangle_it	2.705
r_scbond_it	1.902
r_angle_refined_deg	1.746
r_mcangle_it	1.278
r_mcbond_it	0.825
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.188
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.122
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2544
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing