3QXC | pdb_00003qxc

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QMO	PDB entry 2QMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	20% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; 5% GLYCEROL; 10 MM 8-AMINOOCTANOIC ACID; SOAKED WITH 10 MM ATP, 10 MM MGCL2; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.883	α = 90
b = 37.691	β = 101.24
c = 69.184	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	SBC-3	MIRROR	2008-07-12	M	MOLECULAR REPLACEMENT

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97857	APS	19-BM

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	1.34	50	98.1	0.04	0.04	35.1	3.6	45819	45819		-3	17.2

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	1.34	1.36	83.5		0.4	0.4	2.2	2.5	1964

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2QMO	1.34	50	43464	43464	2319	97.85	0.1402	0.1402	0.13846	0.14	0.17281	0.17	RANDOM	13.683

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]
-0.45		-0.22	0.69		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.823
r_dihedral_angle_4_deg	18.344
r_dihedral_angle_3_deg	11.429
r_dihedral_angle_1_deg	6.38
r_scangle_it	5.909
r_scbond_it	4.448
r_mcangle_it	3.375
r_rigid_bond_restr	2.95
r_mcbond_it	2.705
r_mcbond_other	2.586
r_angle_refined_deg	2.033
r_angle_other_deg	1.223
r_chiral_restr	0.152
r_bond_refined_d	0.026
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1754
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	97

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling