9ERY | pdb_00009ery

Co-crystal strucutre of PD-L1 with low molecular weight inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BIK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.0 M Ammonium sulfate and 0.1 M Sodium cacodylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.534	α = 90
b = 74.534	β = 90
c = 95.392	γ = 120

Symmetry
Space Group	P 31 2 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 EIGER2 X 16M		2023-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03321	PETRA III, DESY	P11

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	2.7	47.7	100	0.087	0.092	0.028	0.999	17.3	19.3		8822

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	2.7	2.83			3.835	4.028	1.226	0.342		20.4

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	2.7	38.36	8797	464	99.943	0.225	0.2217	0.22	0.2755	0.27	119.224

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]
1.45	0.725		1.45		-4.702

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	21.367
r_lrange_it	21.357
r_dihedral_angle_3_deg	18.219
r_scangle_it	17.61
r_scangle_other	17.267
r_dihedral_angle_6_deg	16.952
r_dihedral_angle_2_deg	16.757
r_mcangle_it	14.552
r_mcangle_other	14.548
r_scbond_it	11.747
r_scbond_other	11.545
r_mcbond_it	10.521
r_mcbond_other	10.518
r_dihedral_angle_1_deg	8.979
r_angle_refined_deg	1.811
r_angle_other_deg	0.848
r_chiral_restr_other	0.209
r_xyhbond_nbd_refined	0.204
r_ncsr_local_group_1	0.175
r_nbtor_refined	0.147
r_nbd_refined	0.123
r_symmetry_nbd_refined	0.123
r_symmetry_nbd_other	0.122
r_nbd_other	0.093
r_chiral_restr	0.089
r_symmetry_xyhbond_nbd_refined	0.067
r_symmetry_nbtor_other	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1831
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB-REDO	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction