9Q66 | pdb_00009q66

Human prolyl endopeptidase (PREP) - complex with JP-4-1-7

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
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.853	α = 90
b = 67.294	β = 99.109
c = 158.019	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	2.01	44	93.4	0.273	0.294	0.11	0.99	5.9	7.1		106903			24.4

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	2.01	2.22	54.6		1.53	1.643	0.596	0.33		7.5

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	2.01	44	106903	5347	73.378	0.189	0.1845	0.1849	0.266	0.2664	34.517

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]
0.227		-0.617	-0.232		0.193

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.263
r_dihedral_angle_3_deg	17.767
r_dihedral_angle_6_deg	14.985
r_dihedral_angle_1_deg	9.409
r_dihedral_angle_other_2_deg	7.441
r_lrange_it	5.399
r_lrange_other	5.388
r_scangle_it	3.623
r_scangle_other	3.613
r_mcangle_it	3.056
r_mcangle_other	3.056
r_angle_refined_deg	2.833
r_scbond_it	2.354
r_scbond_other	2.352
r_mcbond_it	1.985
r_mcbond_other	1.966
r_angle_other_deg	0.92
r_symmetry_xyhbond_nbd_refined	0.266
r_symmetry_nbd_refined	0.263
r_nbd_other	0.259
r_nbd_refined	0.236
r_symmetry_nbd_other	0.225
r_nbtor_refined	0.207
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.12
r_symmetry_nbtor_other	0.107
r_symmetry_xyhbond_nbd_other	0.101
r_xyhbond_nbd_other	0.09
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	739
Heterogen Atoms	157

Software

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