8AG1 | pdb_00008ag1

Crystal structure of a novel OX40 antibody

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	5	293	0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.356	α = 90
b = 162.356	β = 90
c = 232.145	γ = 120

Symmetry
Space Group	P 62 2 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 12M		2017-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97853	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.3	77.502	99.7	0.168	0.994	9.1	10.6		27927

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.5			1.945	0.67	1.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2EHY	3.303	77.502	22265	1132	80.148	0.198	0.1943	0.21	0.2681	0.28	91.616

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]
-2.726	-1.363		-2.726		8.842

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	14.564
r_lrange_it	14.563
r_dihedral_angle_6_deg	9.566
r_dihedral_angle_3_deg	9.223
r_mcangle_it	8.38
r_mcangle_other	8.38
r_scangle_it	7.308
r_scangle_other	7.308
r_dihedral_angle_2_deg	5.72
r_mcbond_it	5.523
r_mcbond_other	5.523
r_dihedral_angle_1_deg	4.873
r_scbond_it	4.84
r_scbond_other	4.839
r_rigid_bond_restr	0.683
r_angle_refined_deg	0.593
r_angle_other_deg	0.226
r_nbtor_refined	0.164
r_symmetry_nbd_other	0.162
r_nbd_refined	0.16
r_xyhbond_nbd_refined	0.11
r_symmetry_xyhbond_nbd_refined	0.09
r_symmetry_nbtor_other	0.079
r_nbd_other	0.07
r_symmetry_nbd_refined	0.058
r_chiral_restr	0.027
r_symmetry_xyhbond_nbd_other	0.017
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8016
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing