3IEC | pdb_00003iec

Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		296	Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.466	α = 90
b = 93.256	β = 100.94
c = 113.955	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	103	CCD	ADSC QUANTUM 315r	Beamline X29 features high-flux radiation derived from a 54-pole harmonic emission undulator, a vertically focusing mirror and a horizontally focusing monochromator. A Cryomech AL300 is utilized to produce extremely stable cooling on a Si(111) crystal. The beamline is capable of delivering an energy range of 7-15 kev	2008-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	2.2	50	99.9	0.089	10.5	6.2		97843

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	2.2	2.28	100		0.706		6.2	9784

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	40.96	97422	4890	99.84	0.206	0.204	0.2188	0.248	0.2589	RANDOM	26.151

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]
0.28		0.28	-0.38		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.815
r_dihedral_angle_4_deg	18.5
r_dihedral_angle_3_deg	17.087
r_dihedral_angle_1_deg	6.237
r_scangle_it	3.533
r_scbond_it	2.23
r_angle_refined_deg	1.507
r_mcangle_it	1.442
r_angle_other_deg	0.914
r_mcbond_it	0.768
r_mcbond_other	0.171
r_chiral_restr	0.099
r_bond_refined_d	0.015
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	10625
Nucleic Acid Atoms
Solvent Atoms	687
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection