9BFG

Structure of the crosslinked PCP-E didomain of tyrocidine synthetase A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	295	50 mM MES, 1.8 M ammonium sulfate, 10% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 216.381	α = 90
b = 216.381	β = 90
c = 59.758	γ = 120

Symmetry
Space Group	P 63

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 2M		2023-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	2.18	46.85	100	0.13	0.144	0.062	0.998	13.6	10.3		83879

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	2.18	2.22	100		1.401	1.558	0.674	0.691	1.8	10.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.18	46.85	83867	4242	99.983	0.19	0.1882	0.2283	42.664

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]
0.586	0.293		0.586		-1.902

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.963
r_dihedral_angle_4_deg	18.073
r_dihedral_angle_3_deg	14.59
r_lrange_other	9.813
r_lrange_it	9.812
r_scangle_it	6.976
r_scangle_other	6.975
r_dihedral_angle_1_deg	6.786
r_mcangle_it	5.055
r_mcangle_other	5.055
r_scbond_it	4.669
r_scbond_other	4.668
r_mcbond_it	3.549
r_mcbond_other	3.547
r_angle_refined_deg	1.553
r_angle_other_deg	1.343
r_symmetry_nbd_refined	0.385
r_symmetry_xyhbond_nbd_refined	0.29
r_nbd_other	0.236
r_nbd_refined	0.205
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.14
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8507
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	166

Software

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