4O5J | pdb_00004o5j

Crystal structure of SabA from Helicobacter pylori

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293.15	200mM sodium acetate, 18-20% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
6	79.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.044	α = 90
b = 180.044	β = 90
c = 64.47	γ = 120

Symmetry
Space Group	P 31 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 315r		2013-03-14	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2013-02-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2
2	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9690, 0.9795	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	90.03	100		9.3	60972	60966	1	1	36.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.2	2.32	100		1.03	0.357	2.4	9.3	8825

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.2	90.02	60970	57908	3062	99.95	0.141	0.1409	0.1399	0.1381	0.15939	0.1576	RANDOM	57.126

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]
-0.08	-0.04		-0.08		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	63.685
r_sphericity_bonded	52.249
r_dihedral_angle_2_deg	40.752
r_dihedral_angle_4_deg	20.571
r_dihedral_angle_3_deg	14.509
r_rigid_bond_restr	13.979
r_dihedral_angle_1_deg	4.142
r_angle_refined_deg	1.533
r_chiral_restr	0.09
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2839
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	14

Software

Software
Software Name	Purpose
Blu-Ice	data collection
Auto-Rickshaw	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling