2WQW | pdb_00002wqw

DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER of the Listeria monocytogenes InlB internalin domain

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		9.5	293	293 K. PROTEIN (6.7 MG/ML) PLUS RESERVOIR = 2 PLUS 1. RESERVOIR SOLUTION IS 44-52% PEG2000, 0.1 M CHES PH=9,5, 0.2M NACL., PH 9.5

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.99	α = 90
b = 186.99	β = 90
c = 115.071	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	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.24	50	99.9	0.12	10.5	7.3		37017		-3	37.8

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	2.24	2.36	99.7		0.88	2	6.9

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	2.24	46.88	35166	1849	99.9	0.201	0.199	0.21	0.239	0.24	RANDOM	31.45

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]
-1.09	-0.55		-1.09		1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.12
r_dihedral_angle_4_deg	23.839
r_dihedral_angle_3_deg	16.593
r_dihedral_angle_1_deg	6.952
r_scangle_it	3.233
r_scbond_it	2.165
r_angle_refined_deg	1.909
r_angle_other_deg	1.259
r_mcangle_it	1.12
r_mcbond_it	0.682
r_mcbond_other	0.258
r_chiral_restr	0.13
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4512
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing