9QSM | pdb_00009qsm

small molecule inhibitor in complex with PD-L1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8P1O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1MBis-Tris 6.520% w/v PEG 5000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.521	α = 90
b = 74.996	β = 95.49
c = 74.614	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS3 S 6M		2022-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.75	47.62	99	0.04	0.056	0.038	0.999	13.4	3.4		73948

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)
	1.75	1.78	98.7		0.955	1.299	0.875	0.543	1.2	3.2

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	1.75	47.62	73921	3656	98.847	0.246	0.2443	0.2445	0.2702	0.2713	36.555

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]
-0.482		-2.074	1.077		-0.192

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.914
r_dihedral_angle_6_deg	15.632
r_dihedral_angle_3_deg	13.525
r_lrange_it	9.343
r_dihedral_angle_1_deg	7.69
r_scangle_it	7.201
r_mcangle_it	5.541
r_scbond_it	5.244
r_mcbond_it	4.002
r_angle_refined_deg	2.185
r_nbtor_refined	0.292
r_symmetry_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.201
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.145
r_ncsr_local_group_3	0.123
r_ncsr_local_group_14	0.123
r_ncsr_local_group_13	0.121
r_ncsr_local_group_10	0.119
r_ncsr_local_group_5	0.111
r_ncsr_local_group_1	0.106
r_ncsr_local_group_2	0.106
r_ncsr_local_group_7	0.102
r_ncsr_local_group_12	0.102
r_ncsr_local_group_9	0.098
r_ncsr_local_group_11	0.098
r_ncsr_local_group_15	0.098
r_ncsr_local_group_4	0.097
r_ncsr_local_group_8	0.093
r_ncsr_local_group_6	0.092
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5580
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	147

Software

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