3CYQ

The crystal structure of the complex of the C-terminal domain of Helicobacter pylori MotB (residues 125-256) with N-acetylmuramic acid

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	293	100 mM Tris/HCl, 16-18% PEG 3350, 200 mM sodium tartrate, 10 mM N-acetylmuramic acid, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.781	α = 90
b = 110.058	β = 104.58
c = 113.664	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2007-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9	SLS	X06SA

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	2.3	109.76	96	0.099	7			103524

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	2.3	2.42	98		0.316	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.3	15	103503	5187	96.07	0.22	0.217	0.289	RANDOM	18.046

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]
-1.63		0.22	0.17		1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.056
r_dihedral_angle_4_deg	16.41
r_dihedral_angle_3_deg	15.952
r_scangle_it	6.461
r_dihedral_angle_1_deg	6.217
r_scbond_it	4.87
r_mcangle_it	4.246
r_mcbond_it	3.621
r_angle_refined_deg	1.662
r_angle_other_deg	1.092
r_mcbond_other	1.054
r_symmetry_vdw_refined	0.238
r_symmetry_hbond_refined	0.22
r_symmetry_vdw_other	0.217
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.196
r_nbd_other	0.189
r_nbtor_refined	0.18
r_nbtor_other	0.089
r_chiral_restr	0.082
r_xyhbond_nbd_other	0.033
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17110
Nucleic Acid Atoms
Solvent Atoms	1274
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing