6F3Z | pdb_00006f3z

Complex of E. coli LolA and periplasmic domain of LolC

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NAA	5NAA, 1IWL
experimental model	PDB	1IWL	5NAA, 1IWL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288.15	45% w/v Poly(acrylic acid sodium salt) 2100, 100 mM HEPES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.01	α = 90
b = 68.23	β = 90
c = 94.78	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 6M		2017-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9763	ESRF	ID30B

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	73.01	95.8	0.103	10.6	10.2		61745

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	97		0.844	0.883	2.2	9.9	4379

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	5NAA, 1IWL	2	73.01	58544	3123	95.22	0.2046	0.20222	0.21	0.2492	0.26	RANDOM	45.619

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]
-3.21			0.07		3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.063
r_dihedral_angle_4_deg	16.477
r_dihedral_angle_3_deg	14.245
r_long_range_B_other	9.953
r_long_range_B_refined	9.947
r_scangle_other	7.937
r_dihedral_angle_1_deg	7.216
r_mcangle_it	6.191
r_mcangle_other	6.191
r_scbond_it	5.319
r_scbond_other	5.316
r_mcbond_it	4.337
r_mcbond_other	4.336
r_angle_refined_deg	1.854
r_angle_other_deg	1.061
r_chiral_restr	0.125
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6506
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms

Software

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