4C48 | pdb_00004c48

Crystal structure of AcrB-AcrZ complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DX5	PDB ENTRY 4DX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		CRYSTALLISATION SOLUTION 100 MM HEPES, PH 7.5, 10 MM MGCL2 AND 12% (W/V) PEG 3350. SAMPLE BUFFER 10 MM HEPES PH: 7.5, 50 MM SODIUM CHLORIDE, 0.03% DDM N-DODECYL BETA-D-MALTOPYRANOSIDE

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.01	α = 90
b = 145.01	β = 90
c = 538.34	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	PIXEL	DECTRIS PILATUS			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24		Diamond	I24

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	3.3	30	99.8	0.13	11	5		33271

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	3.3	3.46	100		0.99	1.6	5

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 4DX5	3.3	29.67	31614	1656	99.46	0.28343	0.28142	0.28	0.322	0.33	RANDOM	96.041

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]
1.22	1.22		1.22		-3.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.569
r_dihedral_angle_3_deg	18.149
r_dihedral_angle_4_deg	12.378
r_dihedral_angle_1_deg	7.812
r_angle_refined_deg	1.389
r_angle_other_deg	0.786
r_chiral_restr	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	9259
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	96

Software

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