Experiment: 8PE9

Complex between DDR1 DS-like domain and PRTH-101 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AG4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295.15	0.1 M MES, pH 6.0, 20% (w/v) PEG 6000, 10 mM ZnCl2

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.096	α = 90
b = 144.45	β = 90
c = 52.299	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	PIXEL	DECTRIS EIGER X 16M		2022-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00001	SLS	X10SA

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	3.152	72.225	85.9	0.277	0.3038	0.1224	0.985	7.05	5.97		9760

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)
	3.152	3.562	47.4		1.0737	1.1644	0.4441	0.611	1.79	6.66	488

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4AG4	3.152	72.22	9760	496	61	0.2798	0.2782	0.2755	0.3088	0.3147	RANDOM	68.75

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]
2.5309			5.2089		-7.7397

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	14.8
t_omega_torsion	1.83
t_angle_deg	0.69
t_bond_d	0.004
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4588
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	57

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
BUSTER	refinement
PHASER	phasing