9I5R | pdb_00009i5r

Interactions between Pex3 and Pex19 peptide in yeast

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	ammonium phosphate 0.2M + PEG 3350 20%, ph 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.579	α = 90
b = 137.224	β = 90
c = 111.534	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER X 16M		2023-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97624	PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.62	111.53	100	0.101	0.111	0.045	0.999	11	11.4		16218

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	2.62	2.74			4.759	5.184	2.048	0.394		12.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.62	68.612	16197	844	99.932	0.211	0.2094	0.2097	0.2477	0.2493	110.698

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]
5.35			-0.837		-4.513

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	22.219
r_lrange_other	22.218
r_dihedral_angle_2_deg	18.585
r_scangle_it	17.908
r_scangle_other	17.904
r_dihedral_angle_3_deg	14.553
r_dihedral_angle_6_deg	14.388
r_mcangle_it	12.697
r_mcangle_other	12.694
r_scbond_it	12.35
r_scbond_other	12.348
r_mcbond_it	9.213
r_mcbond_other	9.21
r_dihedral_angle_1_deg	4.818
r_angle_refined_deg	1.631
r_angle_other_deg	0.541
r_nbd_other	0.237
r_nbd_refined	0.233
r_nbtor_refined	0.186
r_symmetry_nbd_other	0.18
r_xyhbond_nbd_refined	0.116
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbd_refined	0.101
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2713
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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