7MMY

Racemic structure of the cyclic plant peptide PDP-23

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7L51

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	Crystals were obtained from a racemic mix of 7mg/ml each of L- and D-peptide in 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% PEG monomethyl ether 2000

Crystal Properties
Matthews coefficient	Solvent content
1.58	22.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.527	α = 90
b = 49.008	β = 92.284
c = 29.402	γ = 90

Symmetry
Space Group	P 1 21/n 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 EIGER X 16M		2020-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.46	49.01	98.8	0.998	10.6	6.4		13346

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.49	80.8		0.833	2.5	6.1

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	7L51	1.464	25.198	13041	619	98.691	0.192	0.1881	0.2763	20.907

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]
-1.867		-0.719	-2.209		4.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.36
r_dihedral_angle_3_deg	10.299
r_rigid_bond_restr	8.917
r_dihedral_angle_1_deg	8.137
r_scangle_it	5.811
r_scangle_other	5.669
r_lrange_other	5.145
r_lrange_it	5.129
r_scbond_it	5.108
r_scbond_other	4.999
r_mcangle_it	3.858
r_mcangle_other	3.854
r_mcbond_it	3.263
r_mcbond_other	3.251
r_angle_refined_deg	1.822
r_angle_other_deg	1.664
r_nbd_other	0.283
r_symmetry_nbd_refined	0.263
r_nbd_refined	0.221
r_nbtor_refined	0.2
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.191
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.111
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	438
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms

Software

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