9Q8L | pdb_00009q8l

Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7WSL
experimental model	PDB	3RRQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Tris pH 8.5, 25% w/v PEG 3,350, 20% w/v MPD

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.839	α = 90
b = 70.241	β = 90
c = 163.684	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M		2024-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-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	1.85	81.84	100	0.106	0.11	0.03	0.999	13.9	13.1		61790			29.7

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	1.85	1.89	100		1.523	1.589	0.448	0.716	1.8	12.4

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	1.85	81.84	61683	3096	99.955	0.18	0.1778	0.1883	0.2159	0.2208	32.183

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]
0.106			-0.21		0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	14.137
r_dihedral_angle_6_deg	13.909
r_dihedral_angle_3_deg	12.714
r_lrange_it	8.093
r_lrange_other	8.093
r_dihedral_angle_1_deg	7.311
r_scangle_it	6.769
r_scangle_other	6.768
r_scbond_it	4.697
r_scbond_other	4.696
r_mcangle_other	3.939
r_mcangle_it	3.938
r_mcbond_it	2.988
r_mcbond_other	2.987
r_angle_other_deg	1.959
r_angle_refined_deg	1.777
r_nbd_other	0.344
r_symmetry_nbd_other	0.223
r_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.187
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.174
r_symmetry_nbd_refined	0.166
r_symmetry_xyhbond_nbd_other	0.133
r_chiral_restr	0.121
r_symmetry_nbtor_other	0.111
r_gen_planes_other	0.015
r_gen_planes_refined	0.014
r_bond_refined_d	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4070
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	115

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing