8AIK | pdb_00008aik

Crystal structure of DltE from L. plantarum, tartare bound form

X-RAY DIFFRACTION

---

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

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.69	α = 90
b = 103.73	β = 90
c = 152.529	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M		2018-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9677	ESRF	ID30B

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	1.95	46.384	99.5	0.05	0.999	14.5	4.5		56946

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	1.95	2			0.564	0.787	2.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8AGR	1.95	46.384	56871	2810	99.338	0.184	0.1825	0.19	0.2211	0.23	30.377

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]
0.011			-0.001		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.935
r_dihedral_angle_2_deg	15.337
r_dihedral_angle_3_deg	15.227
r_lrange_it	7.012
r_lrange_other	7.011
r_dihedral_angle_1_deg	6.226
r_scangle_it	5.716
r_scangle_other	5.715
r_scbond_it	3.791
r_scbond_other	3.787
r_mcangle_it	3.299
r_mcangle_other	3.299
r_mcbond_it	2.53
r_mcbond_other	2.529
r_angle_refined_deg	1.433
r_angle_other_deg	0.869
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.218
r_symmetry_nbd_other	0.196
r_nbd_other	0.188
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.067
r_bond_other_d	0.036
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5006
Nucleic Acid Atoms
Solvent Atoms	572
Heterogen Atoms	30

Software

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