2QMO

Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		273	VAPOR DIFFUSION, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.095	α = 90
b = 37.454	β = 101.48
c = 69.636	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	MIRROR	2007-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	1.47	50	99	0.069	0.069	48.754	7.7	35286	35286		-3	19.8

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	1.47	1.52	91.3		0.444	0.444	3.1	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.47	50	35272	35272	1769	99.03	0.15	0.15	0.148	0.179	RANDOM	16.37

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]
-0.71		-0.58	-0.16		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.92
r_dihedral_angle_4_deg	23.228
r_dihedral_angle_3_deg	11.294
r_dihedral_angle_1_deg	5.866
r_scangle_it	4.139
r_scbond_it	2.896
r_angle_refined_deg	1.715
r_mcangle_it	1.655
r_mcbond_it	1.537
r_angle_other_deg	0.876
r_mcbond_other	0.356
r_symmetry_vdw_other	0.241
r_nbd_refined	0.231
r_nbd_other	0.2
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.162
r_chiral_restr	0.118
r_symmetry_vdw_refined	0.105
r_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.003
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1729
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	2

Software

Software
Software Name	Purpose
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
SHELXE	model building
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing