2Q1S | pdb_00002q1s

Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NADH

X-RAY DIFFRACTION

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, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.186	α = 90
b = 77.875	β = 108.19
c = 59.411	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	1.5	50	99.3	0.052	29.5	4.8	57672	57271		1.8	31.5

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	1.5	1.53	94.8		0.658	1.83	3.7	2698

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	1.5	38.52	57672	54327	2854	99.19	0.194	0.19358	0.19185	0.18	0.22622	RANDOM	43.882

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]
-0.06		-0.6	1.2		-1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.382
r_dihedral_angle_4_deg	23.914
r_dihedral_angle_3_deg	13.313
r_dihedral_angle_1_deg	10.184
r_scangle_it	2.86
r_scbond_it	2.026
r_angle_refined_deg	1.617
r_mcangle_it	1.588
r_mcbond_it	0.989
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.382
r_dihedral_angle_4_deg	23.914
r_dihedral_angle_3_deg	13.313
r_dihedral_angle_1_deg	10.184
r_scangle_it	2.86
r_scbond_it	2.026
r_angle_refined_deg	1.617
r_mcangle_it	1.588
r_mcbond_it	0.989
r_nbtor_refined	0.308
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.169
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.111
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2564
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	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 R01GM157729.