7OFV

NMR-guided design of potent and selective EphA4 agonistic ligands

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.10 M Na Acet, pH 4.50, 1.20 M K2HPO4, 0.80 M NaH2PO4

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.032	α = 90
b = 55.032	β = 90
c = 147.313	γ = 90

Symmetry
Space Group	P 43 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	100	PIXEL	DECTRIS PILATUS 6M		2017-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.0332	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.43	51.552	93.8	0.053	0.053	0.055	0.015	1	24.9	12.9		34710

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.43	1.544	57.1		0.883	0.883	1.012	0.48	0.534	1.2	4

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	5JR2	1.43	51.547	34710	1715	81.002	0.152	0.149	0.2065	20.129

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]
-0.066			-0.066		0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	35.574
r_dihedral_angle_2_deg	30.957
r_dihedral_angle_other_6_deg	16.29
r_dihedral_angle_4_deg	14.844
r_dihedral_angle_6_deg	14.682
r_dihedral_angle_3_deg	11.43
r_dihedral_angle_1_deg	7.087
r_lrange_it	4.434
r_lrange_other	4.043
r_scangle_it	3.898
r_scangle_other	3.897
r_scbond_it	3.555
r_scbond_other	3.554
r_mcangle_it	3.195
r_mcangle_other	3.193
r_mcbond_it	2.948
r_mcbond_other	2.888
r_rigid_bond_restr	2.283
r_dihedral_angle_other_2_deg	1.592
r_angle_refined_deg	1.562
r_angle_other_deg	1.461
r_symmetry_nbd_other	0.177
r_nbd_refined	0.173
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.154
r_nbd_other	0.129
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.071
r_symmetry_nbd_refined	0.06
r_bond_refined_d	0.009
r_bond_other_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1558
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing