2XD9

STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-Trihydroxy-2-((E)-prop-1- enyl)-4,5,6,7-tetrahydrobenzo(b)thiophene-4-carboxylic acid

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C4V	PDB ENTRY 2C4V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.8		50 MM TRIS-HCL PH 7.5 1 MM 2-MERCAPTOETHANOL 1 MM ETHYLENEDIAMINETETRAACETIC ACID 200 MM SODIUM CHLORIDE 24% (W/V) POLYETHYLENEGLYCOL 4000 100 MM SODIUM CITRATE, PH 5.8 12.5 MM (4R, 6R, 7S)-4,6, 7-TRIHYDROXY-2-[(E)-PROP-1-ENYL]-4,5,6, 7-TETRAHYDROBENZO[B]THIOPHENE-4-CARBOXYLIC ACID 0.13 % (V/V) METHANOL

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.217	α = 90
b = 100.217	β = 90
c = 103.934	γ = 90

Symmetry
Space Group	P 42 2 2

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 CCD		2009-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.95	34	98.7	0.08	5.8	12.5		38626			24.2

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	1.95	2.06	99.7		0.36	1.8	12.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2C4V	1.95	15	36894	1536	99.55	0.21218	0.2105	0.25025	THIN SHELLS	25.237

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]
-0.75			-0.75		1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.521
r_dihedral_angle_3_deg	15.433
r_dihedral_angle_4_deg	8.672
r_dihedral_angle_1_deg	5.752
r_scangle_it	3.262
r_scbond_it	2.143
r_mcangle_it	1.717
r_angle_refined_deg	1.449
r_mcbond_it	0.973
r_angle_other_deg	0.894
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.205
r_mcbond_other	0.189
r_xyhbond_nbd_refined	0.182
r_nbd_other	0.181
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.155
r_symmetry_vdw_other	0.144
r_chiral_restr	0.09
r_nbtor_other	0.086
r_xyhbond_nbd_other	0.017
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3528
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing