9Q5X | pdb_00009q5x

Human prolyl endopeptidase (PREP) - complex with KT-2-74

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
2.18	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.822	α = 90
b = 66.473	β = 102.067
c = 156.856	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	1.41	34.6	93.5	0.173	0.187	0.07	1	7.5	7		320614			11.5

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	48.6		2.022	2.172	0.792	0.27	1.4	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	1.41	34.6	320614	16132	80.072	0.157	0.1551	0.155	0.1922	0.1922	18.008

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]
-0.031		0.045	0.025		-0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.394
r_dihedral_angle_2_deg	15.211
r_dihedral_angle_3_deg	12.947
r_dihedral_angle_1_deg	6.903
r_lrange_other	6.195
r_lrange_it	6.194
r_scangle_it	4.163
r_scangle_other	4.163
r_dihedral_angle_other_2_deg	3.886
r_scbond_it	2.813
r_scbond_other	2.813
r_angle_refined_deg	2.181
r_mcangle_it	1.86
r_mcangle_other	1.86
r_mcbond_it	1.279
r_mcbond_other	1.255
r_angle_other_deg	0.753
r_symmetry_xyhbond_nbd_refined	0.338
r_symmetry_nbd_refined	0.303
r_symmetry_xyhbond_nbd_other	0.27
r_nbd_refined	0.219
r_nbd_other	0.215
r_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.185
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.087
r_xyhbond_nbd_other	0.054
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	17030
Nucleic Acid Atoms
Solvent Atoms	2323
Heterogen Atoms	304

Software

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