9Q65 | pdb_00009q65

Human prolyl endopeptidase (PREP) - complex with KT-2-75

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		277	25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.522	α = 90
b = 65.986	β = 100.473
c = 159.33	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		2024-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979338	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	1.89	34.6	91.7	0.37	0.399	0.149	0.98	4.6	7.1		121039			20.6

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	1.89	2.08	58.1		1.447	1.558	0.576	0.22		7.3

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	1.89	34.6	121039	6051	69.672	0.222	0.2184	0.1883	0.2954	0.2555	17.884

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]
0.077		2.485	-2.125		2.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.597
r_dihedral_angle_3_deg	15.878
r_dihedral_angle_6_deg	14.841
r_dihedral_angle_1_deg	8.21
r_dihedral_angle_other_2_deg	6.693
r_lrange_it	2.244
r_lrange_other	2.244
r_angle_refined_deg	2.058
r_scangle_it	1.653
r_scangle_other	1.653
r_mcangle_it	1.614
r_mcangle_other	1.614
r_scbond_it	1.163
r_scbond_other	1.163
r_mcbond_it	1.145
r_mcbond_other	1.144
r_angle_other_deg	0.671
r_nbd_other	0.279
r_symmetry_xyhbond_nbd_refined	0.266
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.23
r_symmetry_nbd_other	0.213
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.186
r_xyhbond_nbd_other	0.133
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16992
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	161

Software

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