9Q6K | pdb_00009q6k

Human prolyl endopeptidase (PREP) - complex with JP-2-1-7

X-RAY DIFFRACTION

---

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
2.17	43.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.337	α = 90
b = 66.845	β = 102.073
c = 155.637	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	1.85	42.7	94.1	0.26	0.28	0.15	0.99	6.1	7.1		131193			22.6

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	1.85	2.03	57.3		1.553	1.67	0.886	0.86	1.4	7.4

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	1.85	42.7	131193	6494	74.408	0.2	0.1964	0.196	0.2716	0.2716	30.465

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]
-0.011		0.17	-0.559		0.455

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.892
r_dihedral_angle_3_deg	16.191
r_dihedral_angle_6_deg	15.346
r_dihedral_angle_1_deg	8.655
r_dihedral_angle_other_2_deg	6.021
r_lrange_it	5.901
r_lrange_other	5.901
r_scangle_it	3.718
r_scangle_other	3.699
r_mcangle_it	2.724
r_mcangle_other	2.724
r_angle_refined_deg	2.673
r_scbond_it	2.459
r_scbond_other	2.451
r_mcbond_it	1.806
r_mcbond_other	1.756
r_angle_other_deg	0.869
r_nbd_other	0.255
r_nbd_refined	0.243
r_symmetry_xyhbond_nbd_other	0.236
r_symmetry_nbd_other	0.22
r_symmetry_xyhbond_nbd_refined	0.211
r_xyhbond_nbd_refined	0.203
r_nbtor_refined	0.201
r_symmetry_nbd_refined	0.2
r_chiral_restr	0.119
r_symmetry_nbtor_other	0.1
r_bond_refined_d	0.016
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	967
Heterogen Atoms	264

Software

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