9Q5Z | pdb_00009q5z

Human prolyl endopeptidase (PREP) - complex with KT-1-147

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 = 103.534	α = 90
b = 66.37	β = 101.983
c = 156.046	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 16M		2024-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97934	NSLS-II	17-ID-2

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	1.41	34.1	93.9	0.083	0.101	0.056	1	1.6	3.1		306553			14.5

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	1.41	1.53	58.8		0.842	1	0.536	0.56	1.6

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	1.41	34.1	306553	15344	76.227	0.154	0.1522	0.1521	0.1866	0.1866	19.445

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]
-0.024		0.029	0.041		-0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.186
r_dihedral_angle_6_deg	15.683
r_dihedral_angle_3_deg	12.751
r_dihedral_angle_1_deg	6.751
r_lrange_it	5.908
r_lrange_other	5.908
r_dihedral_angle_other_2_deg	4.479
r_scangle_it	4.367
r_scangle_other	4.367
r_scbond_it	2.933
r_scbond_other	2.933
r_angle_refined_deg	2.178
r_mcangle_it	1.994
r_mcangle_other	1.994
r_mcbond_it	1.446
r_mcbond_other	1.423
r_angle_other_deg	0.748
r_symmetry_xyhbond_nbd_refined	0.241
r_nbd_other	0.232
r_nbd_refined	0.216
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.184
r_symmetry_nbd_refined	0.184
r_chiral_restr	0.111
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.08
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	17031
Nucleic Acid Atoms
Solvent Atoms	2226
Heterogen Atoms	344

Software

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