2WQV | pdb_00002wqv

Internalin domain of Listeria monocytogenes InlB: rhombohedral crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H6T	PDB ENTRY 1H6T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	SITTING VAPOR DIFFUSION AT 293 K. 200 NL PROTEIN PLUS 100 NL OF RESERVOIR SOLUTION CONSISTING OF 0.1 M NACL, 0.1 M CHES PH 9.5, 40% PEG300. THE PROTEIN WAS ACTUALLY A COMPLEX OF MET741 WITH INLB321 AT 5 MG/ML, I.E. INLB321 WAS AT 1.4 MG/ML. CRYSTAL GROWTH TIME: SEVERAL WEEKS TO MONTHS.

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.9	α = 90
b = 185.9	β = 90
c = 115.07	γ = 120

Symmetry
Space Group	H 3 2

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	MARRESEARCH		2006-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.8	20	99.3	0.16	10.98	6.96		18763		-3	45.1

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	2.8	2.87	100		0.91	2.58	7.08

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	PDB ENTRY 1H6T	2.8	19.822	18762	941	99.692	0.205	0.2033	0.21	0.2378	0.25	RANDOM	40.35

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]
2.278	1.139		2.278		-3.417

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.594
r_dihedral_angle_3_deg	14.609
r_dihedral_angle_4_deg	13.99
r_dihedral_angle_1_deg	5.979
r_scangle_it	1.11
r_angle_refined_deg	1.072
r_angle_other_deg	0.815
r_scbond_it	0.771
r_mcangle_it	0.387
r_mcbond_it	0.334
r_symmetry_vdw_other	0.212
r_nbd_refined	0.195
r_nbd_other	0.185
r_nbtor_refined	0.168
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.137
r_symmetry_vdw_refined	0.125
r_nbtor_other	0.082
r_chiral_restr	0.057
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4436
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing