2Q1U | pdb_00002q1u

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	2PZJ	The starting model was the related PDB entry 2PZJ, the same protein in a different crystal form. The biological unit (i.e. a dimer), generated from crystallographic symmetry, was used as the search model.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M Tris, 0.2 M calcium acetate, 20 % (w/v) PEG 3000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.851	α = 90
b = 79.682	β = 113.1
c = 84.953	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	1.7	50	98.4	0.055	21.9	3.9	82675	81311		2	23.3

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	1.7	1.73	87.1		0.459	2.18	2.9	4064

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	The starting model was the related PDB entry 2PZJ, the same protein in a different crystal form. The biological unit (i.e. a dimer), generated from crystallographic symmetry, was used as the search model.	1.7	50	82675	81311	4061	98.16	0.177	0.17736	0.177	0.1756	0.211	RANDOM	20.913

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]
-1.96		-1.01	1.77		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.584
r_dihedral_angle_4_deg	22.43
r_dihedral_angle_3_deg	12.383
r_dihedral_angle_1_deg	8.731
r_scangle_it	2.908
r_scbond_it	2.001
r_angle_refined_deg	1.538
r_mcangle_it	1.302
r_mcbond_it	0.887
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.25
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.134
r_symmetry_vdw_refined	0.13
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5091
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	142

Software

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