3CYP | pdb_00003cyp

The crystal structure of the C-terminal domain of Helicobacter pylori MotB (residues 125-256).

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, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.816	α = 90
b = 89.479	β = 112.55
c = 66.322	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)	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	1.6	61.2	99.6	0.071	0.071	5.9	3.8		71913

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)
	1.6	1.69	100		0.398	0.398	1.9	3.7	10555

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.6	50.572	71888	3630	99.61	0.188	0.185	0.19	0.227	0.23	RANDOM	17.895

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]
-0.3		-0.07	0.46		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.28
r_dihedral_angle_4_deg	18.07
r_dihedral_angle_3_deg	13.969
r_dihedral_angle_1_deg	5.995
r_scangle_it	3.673
r_scbond_it	2.544
r_mcangle_it	1.576
r_angle_refined_deg	1.494
r_mcbond_it	1.448
r_angle_other_deg	0.963
r_mcbond_other	0.258
r_symmetry_vdw_other	0.231
r_nbd_refined	0.228
r_nbd_other	0.198
r_symmetry_hbond_refined	0.186
r_nbtor_refined	0.185
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.093
r_nbtor_other	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4357
Nucleic Acid Atoms
Solvent Atoms	611
Heterogen Atoms

Software

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