6GBG | pdb_00006gbg

Helicobacter pylori adhesin HopQ type I bound to the N-terminal domain of human CEACAM1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LP2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Condition B3 of the Morpheus HT-96 screen (Molecular Dimensions)(0.09 M Halogens mix (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (1.0M Imidazole; MES monohydrate (acid); pH 6.5), 50 % v/v Precipitant Mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.43	α = 90
b = 94.43	β = 90
c = 119.7	γ = 120

Symmetry
Space Group	P 32 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	PIXEL	DECTRIS PILATUS 6M		2016-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.98	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.8	67.52	100	0.147	0.047	0.998	13.6	10.5		15692			73.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	99.6		0.538	0.628	1.6	10.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5LP2	2.8	67.52	14860	807	99.91	0.20471	0.20131	0.21	0.26328	0.26	RANDOM	71.153

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]
0.64	0.32		0.64		-2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.573
r_dihedral_angle_3_deg	18.261
r_dihedral_angle_4_deg	13.315
r_dihedral_angle_1_deg	7.102
r_long_range_B_refined	5.683
r_long_range_B_other	5.682
r_scangle_other	3.806
r_mcangle_it	3.156
r_mcangle_other	3.156
r_scbond_it	2.315
r_scbond_other	2.314
r_mcbond_it	1.943
r_mcbond_other	1.942
r_angle_refined_deg	1.457
r_angle_other_deg	0.782
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3271
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing