8D5J | pdb_00008d5j

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VGK	PDB entry 1VGK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277.15	20% w/v PEG3000, 100 mM HEPES, 200 mM sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.4336634	49.490311

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.44	α = 90
b = 66.57	β = 92.01
c = 56.96	γ = 90

Symmetry
Space Group	C 1 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 EIGER X 16M		2020-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-E	0.98	APS	21-ID-E

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	1.95	40.902	97.1	0.138	0.173	0.103	0.991	15.9	4.7		30593

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	1.95	2			0.74	0.954	0.594	0.682		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VGK	1.95	40.902	30593	1561	96.868	0.188	0.186	0.2	0.2297	0.24	39.061

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]
-0.596		0.062	0.595		-0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.761
r_dihedral_angle_3_deg	15.184
r_dihedral_angle_2_deg	12.567
r_lrange_it	8.419
r_dihedral_angle_1_deg	6.622
r_scangle_it	6.137
r_scbond_it	4.027
r_mcangle_it	3.907
r_mcbond_it	2.666
r_angle_refined_deg	1.701

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.761
r_dihedral_angle_3_deg	15.184
r_dihedral_angle_2_deg	12.567
r_lrange_it	8.419
r_dihedral_angle_1_deg	6.622
r_scangle_it	6.137
r_scbond_it	4.027
r_mcangle_it	3.907
r_mcbond_it	2.666
r_angle_refined_deg	1.701
r_nbtor_refined	0.312
r_symmetry_xyhbond_nbd_refined	0.253
r_symmetry_nbd_refined	0.227
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.111
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3151
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
BUCCANEER	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.