2Y5P | pdb_00002y5p

B-repeat of Listeria monocytogenes InlB (internalin B)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	20 DEG C IN HANGING OR SITTING-DROPS WITH 2 UL PROTEIN (17.3 MG/ML) PLUS 1 UL RESERVOIR (0.1 M NA-ACETATE PH 5.0, 0.2 M CACL2, 18 % PEG 6000).

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.61	α = 90
b = 58.34	β = 90
c = 158.07	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR555 FLAT PANEL			M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD			M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12		EMBL/DESY, HAMBURG	X12

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	1.3	47	99.9	0.07	31.8	22.7		66287		-3	21

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	1.3	1.33	99.3		0.72	2.98

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	MAD	THROUGHOUT	NONE	1.3	47	64294	1989	99.9	0.15827	0.15709	0.17	0.19559	0.2	RANDOM	18.105

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]
3.24			-1.85		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.57
r_dihedral_angle_4_deg	20.013
r_dihedral_angle_3_deg	12.67
r_scangle_it	7.014
r_dihedral_angle_1_deg	6.355
r_scbond_it	5.148
r_mcangle_it	3.841
r_mcbond_it	2.693
r_rigid_bond_restr	2.409
r_angle_refined_deg	2.097
r_mcbond_other	1.112
r_angle_other_deg	1.003
r_chiral_restr	0.127
r_bond_refined_d	0.024
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2313
Nucleic Acid Atoms
Solvent Atoms	396
Heterogen Atoms	11

Software

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