9XYK | pdb_00009xyk

Human prolyl endopeptidase (PREP) - complex with JP-7-1-7

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
2.16	43.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.543	α = 90
b = 66.302	β = 102.102
c = 156.244	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		2025-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.919901	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	1.73	34.5	93.9	0.358	0.387	0.144	0.99	4.7	7.1		139379			15.1

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	1.73	1.99	55.7		1.472	1.587	0.588	0.5	1.5	7.2

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	1.73	34.5	139379	6975	64.265	0.192	0.1891	0.157	0.2554	0.214	18.159

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]
-0.535		-0.165	-1.786		2.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.899
r_dihedral_angle_6_deg	14.697
r_dihedral_angle_2_deg	12.885
r_dihedral_angle_1_deg	7.91
r_lrange_it	3.109
r_lrange_other	3.034
r_scangle_it	2.005
r_scangle_other	2.005
r_angle_refined_deg	1.998
r_mcangle_it	1.522
r_mcangle_other	1.522
r_scbond_it	1.321
r_scbond_other	1.321
r_mcbond_it	1.042
r_mcbond_other	1.035
r_angle_other_deg	0.663
r_symmetry_xyhbond_nbd_refined	0.271
r_xyhbond_nbd_refined	0.234
r_nbd_other	0.232
r_nbd_refined	0.21
r_symmetry_nbd_other	0.206
r_symmetry_nbd_refined	0.196
r_nbtor_refined	0.189
r_symmetry_xyhbond_nbd_other	0.095
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.089
r_xyhbond_nbd_other	0.016
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	1638
Heterogen Atoms	413

Software

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