8JYG

Crystal structure of Human HPSE1 in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E8M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	25% w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.38	α = 90
b = 71.049	β = 98.09
c = 78.28	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 PILATUS3 6M		2018-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00003	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	77.5	99.8	0.993	7.5	5.3		32623

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.79

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5E8M	2	43.977	32605	1600	99.807	0.168	0.1656	0.2092	32.783

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]
-0.678		1.313	-3.109		3.282

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.751
r_dihedral_angle_4_deg	21.087
r_dihedral_angle_3_deg	14.579
r_lrange_it	8.651
r_lrange_other	8.651
r_dihedral_angle_1_deg	7.204
r_scangle_it	4.948
r_scangle_other	4.948
r_mcangle_other	3.939
r_mcangle_it	3.935
r_scbond_it	3.2
r_scbond_other	3.199
r_mcbond_it	2.593
r_mcbond_other	2.57
r_angle_refined_deg	1.582
r_angle_other_deg	1.273
r_symmetry_xyhbond_nbd_refined	0.234
r_nbd_other	0.217
r_nbd_refined	0.201
r_symmetry_nbd_other	0.184
r_symmetry_nbd_refined	0.177
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.168
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.017
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3644
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	146

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing