9Q6J | pdb_00009q6j

Human prolyl endopeptidase (PREP) - complex with KT-2-126

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.127	α = 90
b = 66.936	β = 99.284
c = 157.183	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	100	PIXEL	DECTRIS EIGER X 9M		2025-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.919764	NSLS-II	17-ID-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	43.8	94.2	0.241	0.26	0.099	0.99	6.4	6.8		167666			16.4

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	1.75	1.93	57.7		1.544	1.677	0.647	0.64	1.4

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	1.75	43.8	167665	8371	76.589	0.167	0.1642	0.1644	0.2261	0.2265	23.884

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]
0.244		-0.142	-0.36		0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.979
r_dihedral_angle_6_deg	15.335
r_dihedral_angle_3_deg	14.228
r_dihedral_angle_other_2_deg	8.251
r_dihedral_angle_1_deg	7.566
r_lrange_it	5.824
r_lrange_other	5.762
r_scangle_it	3.614
r_scangle_other	3.614
r_angle_refined_deg	2.411
r_scbond_it	2.406
r_scbond_other	2.406
r_mcangle_it	2.057
r_mcangle_other	2.057
r_mcbond_it	1.367
r_mcbond_other	1.344
r_angle_other_deg	0.804
r_symmetry_nbd_refined	0.271
r_symmetry_xyhbond_nbd_refined	0.268
r_nbd_other	0.255
r_nbd_refined	0.215
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.191
r_symmetry_xyhbond_nbd_other	0.159
r_chiral_restr	0.112
r_symmetry_nbtor_other	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17019
Nucleic Acid Atoms
Solvent Atoms	1853
Heterogen Atoms	324

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing