8D5K

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide 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		277.15	10% w/v PEG8000, 200 mM magnesium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.4348	49.5142

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.37	α = 90
b = 66.2	β = 92.42
c = 56.79	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		2020-06-10	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	41.349	90.4	0.069	0.096	0.067	0.993	14.6	2.3		23784

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	97		0.281	0.396	0.278	0.899		1.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VGK	2.066	41.349	23784	1254	90.245	0.204	0.2027	0.2335	46.908

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]
-0.426		0.163	3.235		-2.812

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.388
r_dihedral_angle_3_deg	16.067
r_lrange_it	8.08
r_dihedral_angle_1_deg	7.677
r_scangle_it	5.805
r_dihedral_angle_2_deg	5.714
r_scbond_it	4.248
r_mcangle_it	4.188
r_mcbond_it	3.064
r_angle_refined_deg	1.874

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.388
r_dihedral_angle_3_deg	16.067
r_lrange_it	8.08
r_dihedral_angle_1_deg	7.677
r_scangle_it	5.805
r_dihedral_angle_2_deg	5.714
r_scbond_it	4.248
r_mcangle_it	4.188
r_mcbond_it	3.064
r_angle_refined_deg	1.874
r_symmetry_nbd_refined	0.501
r_symmetry_xyhbond_nbd_refined	0.326
r_nbtor_refined	0.316
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.12
r_gen_planes_refined	0.009
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3139
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms

Software

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

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.