4CDI | pdb_00004cdi

Crystal structure of AcrB-AcrZ complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4C48	PDB ENTRY 4C48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	THE ACRBZ COMPLEX AT 10 MG ML-1 USING SAMPLE BUFFER. 9 MM N-OCTYL-BETA-D-THIOGLUCOPYRANOSIDE (90 MM) WAS MIXED WITH ACRBZ COMPLEX BEFORE THE CRYSTALLISATION TRIALS. THE ACRBZ CRYSTALS WERE GROWN AT 20 C USING THE HANGING-DROPLET VAPOUR DIFFUSION METHOD BY MIXING 4 MICROLITERS OF ACRBZ COMPLEX WITH 2 MICROLITERS OF RESERVOIR SOLUTION (100 MM TRICINE PH: 7.4, 50 MM LITHIUM SULPHATE, 5 MM CADMIUM CHLORIDE HYDRATE, 7 % PEG 3000, 10% GLYCEROL).

Crystal Properties
Matthews coefficient	Solvent content
4.51	72.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.205	α = 90
b = 146.205	β = 90
c = 543.207	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 2M		2013-01-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PIXEL		2013-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24		Diamond	I24
2	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	3.69	24.89	94.5	0.13	15.1	10.6		23077		2	148

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	3.69	3.99	94.8		1.17	2.1	10.6

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 4C48	3.7	24.91	21912	1161	94.04	0.34009	0.33906	0.34	0.36127	0.35	RANDOM	117.759

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]
3.41	3.41		3.41		-11.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.188
r_dihedral_angle_3_deg	18.157
r_dihedral_angle_4_deg	12.295
r_dihedral_angle_1_deg	7.88
r_mcangle_it	1.582
r_angle_refined_deg	1.398
r_mcbond_it	1.123
r_mcbond_other	1.123
r_scbond_it	1.114
r_angle_other_deg	0.818
r_chiral_restr	0.072
r_bond_refined_d	0.01
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_mcangle_other
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	8114
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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