3BZ5 | pdb_00003bz5

Functional domain of InlJ from Listeria monocytogenes includes a cysteine ladder

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O6V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	298	2M Ammonium sulfate, 0.1M Na acetate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.272	α = 90
b = 159.272	β = 90
c = 159.272	γ = 90

Symmetry
Space Group	I 2 3

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	MAR CCD 165 mm	Si [111], horizontally focussing	2006-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.817	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.7	21.28	99.9	0.112	0.112	17.9	11.2	18505	18486	1	1	49.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.8			0.391	0.391	5.3	7.1	1809

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1O6V	2.7	21.28	18505	17059	919	97.17	0.18512	0.18152	0.2	0.25261	0.26	RANDOM	16.976

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.172
r_dihedral_angle_3_deg	12.189
r_dihedral_angle_1_deg	5.712
r_scangle_it	4.312
r_mcangle_it	3.968
r_dihedral_angle_4_deg	3.287
r_mcbond_it	3.151
r_scbond_it	3.145
r_angle_refined_deg	1.815
r_angle_other_deg	1.733
r_mcbond_other	0.517
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.172
r_symmetry_vdw_other	0.154
r_nbd_other	0.153
r_nbtor_refined	0.142
r_xyhbond_nbd_refined	0.121
r_symmetry_hbond_refined	0.112
r_nbtor_other	0.069
r_chiral_restr	0.062
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3498
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing