9Q62 | pdb_00009q62

Human prolyl endopeptidase (PREP) - complex with KT-2-108

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
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.189	α = 90
b = 67.075	β = 99.198
c = 157.164	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	1.83	43.9	92.1	0.237	0.256	0.097	0.99	6.6	6.8		144444			17.8

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	1.83	2			1.42	1.536	0.589	0.38	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	1.83	43.9	144443	7173	74.441	0.177	0.1734	0.1735	0.2395	0.2399	25.592

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]
0.133		-0.067	-0.039		-0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.297
r_dihedral_angle_3_deg	16.122
r_dihedral_angle_6_deg	15.198
r_dihedral_angle_1_deg	8.141
r_lrange_it	5.515
r_lrange_other	5.515
r_scangle_it	3.256
r_scangle_other	3.256
r_dihedral_angle_other_2_deg	3.116
r_angle_refined_deg	2.57
r_mcangle_it	2.495
r_mcangle_other	2.495
r_scbond_it	2.181
r_scbond_other	2.181
r_mcbond_it	1.641
r_mcbond_other	1.597
r_angle_other_deg	0.841
r_nbd_other	0.313
r_symmetry_nbd_refined	0.277
r_nbd_refined	0.232
r_symmetry_nbd_other	0.214
r_symmetry_xyhbond_nbd_refined	0.213
r_xyhbond_nbd_refined	0.202
r_nbtor_refined	0.196
r_metal_ion_refined	0.172
r_symmetry_xyhbond_nbd_other	0.146
r_chiral_restr	0.115
r_symmetry_nbtor_other	0.101
r_xyhbond_nbd_other	0.046
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	1389
Heterogen Atoms	268

Software

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