8AJI

Crystal structure of DltE from L. plantarum, TCEP form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8AGR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 3350, ammonium tartrate, TCEP HCl

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.236	α = 90
b = 98.642	β = 105.799
c = 135.934	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M		2018-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873130	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.94	49.501	97.7	0.095	0.988	5.3	3.8		139757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.97			0.395	0.811

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8AGR	1.94	49.501	139693	1994	97.569	0.184	0.1833	0.2124	24.243

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]
-0.014		-0.003	0.001		0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.706
r_dihedral_angle_3_deg	14.611
r_dihedral_angle_2_deg	6.635
r_lrange_it	6.554
r_lrange_other	6.473
r_dihedral_angle_1_deg	6.031
r_scangle_it	4.903
r_scangle_other	4.902
r_scbond_it	3.267
r_scbond_other	3.267
r_mcangle_it	3.086
r_mcangle_other	3.086
r_mcbond_it	2.286
r_mcbond_other	2.284
r_angle_refined_deg	1.397
r_angle_other_deg	0.774
r_nbd_other	0.247
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.183
r_symmetry_nbd_refined	0.18
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_other	0.154
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.076
r_bond_other_d	0.036
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10510
Nucleic Acid Atoms
Solvent Atoms	1210
Heterogen Atoms	126

Software

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