7AG5

Structure of the Laspartomycin C double mutant G4D D-allo-Thr9D-Dap in complex with Geranyl phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.2 M sodium formate, 40% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.428	α = 90
b = 40.428	β = 90
c = 31.033	γ = 120

Symmetry
Space Group	P 6 2 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 6M-F		2019-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.031	35.012	92.2	0.185	0.193	0.054	0.997	8	11.7		6321

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.031	1.116	53.1		1.584	1.664	0.504	0.726	1.5	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5O0Z	1.04	35.01	6011	299	82.66	0.1215	0.1204	0.1432	RANDOM	16.751

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]
0.69	0.35		0.69		-2.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	67.91
r_dihedral_angle_2_deg	24.766
r_dihedral_angle_3_deg	12.913
r_rigid_bond_restr	2.465
r_angle_refined_deg	1.721
r_angle_other_deg	0.662
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	67.91
r_dihedral_angle_2_deg	24.766
r_dihedral_angle_3_deg	12.913
r_rigid_bond_restr	2.465
r_angle_refined_deg	1.721
r_angle_other_deg	0.662
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	91
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Aimless	data scaling
STARANISO	data scaling
DIALS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.