2PZJ

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

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	0.1 M bicine, 16 % (w/w) PEG 8000, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.884	α = 90
b = 77.875	β = 108.17
c = 59.226	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	1.9	50	96.6	0.039	32.1	4.6	28232	27275		5	24.88

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	1.9	1.93	77.4		0.223	5.89	3	1061

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	PDB entries 1BXK, 1KEU, 1R6D	1.9	38.38	28232	25919	1352	96.48	0.163	0.16305	0.16086	0.20428	RANDOM	23.931

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]
0.31		-0.73	1.12		-1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.072
r_dihedral_angle_4_deg	20.746
r_dihedral_angle_3_deg	14.511
r_dihedral_angle_1_deg	6.084
r_scangle_it	2.324
r_scbond_it	1.629
r_angle_refined_deg	1.458
r_angle_other_deg	1.003
r_mcangle_it	0.913
r_mcbond_it	0.651
r_symmetry_vdw_other	0.257
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.21
r_nbd_other	0.196
r_mcbond_other	0.176
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.087
r_xyhbond_nbd_other	0.087
r_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2519
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	44

Software

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