2WQX | pdb_00002wqx

InlB321_4R: S199R, D200R, G206R, A227R, C242A mutant 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	VAPOR DIFFUSION, SITTING DROP		293	SITTING DROP VAPOUR DIFFUSION AT 293K WITH 1 UL PROTEIN (3.8 MG/ML IN 50 MM HEPES, PH 7.0, 100 MM NACL) PLUS 0.5 UL RESERVOIR (17% PEG1000MME, 90 MM NA-CITRATE).

Crystal Properties
Matthews coefficient	Solvent content
2.14	0.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.7	α = 102.99
b = 57.45	β = 90.21
c = 64.3	γ = 93.56

Symmetry
Space Group	P 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	CCD	RIGAKU SATURN 944PLUS	VARIMAX HF	2009-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	2.03	20	96.8	0.12	12.65	5.1		33525		-3	20.09

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	2.03	2.09	68.5		0.41	4.02	3.7

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	PDB ENTRY 1H6T	2.03	38.63	31849	1677	100	0.19729	0.19423	0.21	0.2567	0.27	RANDOM	12.299

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]
-0.38	0.24	0.15	0.93	-0.01	-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.146
r_dihedral_angle_4_deg	19.117
r_dihedral_angle_3_deg	14.752
r_dihedral_angle_1_deg	6.969
r_scangle_it	4.098
r_scbond_it	2.543
r_angle_refined_deg	1.799
r_mcangle_it	1.46
r_angle_other_deg	1.081
r_mcbond_it	0.85
r_mcbond_other	0.274
r_chiral_restr	0.109
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
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	4546
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms

Software

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