8JYG

Crystal structure of Human HPSE1 in complex with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E8M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.529325% w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.3647.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.38α = 90
b = 71.049β = 98.09
c = 78.28γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00003SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1277.599.80.9937.55.332623
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.050.79

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5E8M243.97732605160099.8070.1680.16560.209232.783
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]
-0.6781.313-3.1093.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.751
r_dihedral_angle_4_deg21.087
r_dihedral_angle_3_deg14.579
r_lrange_it8.651
r_lrange_other8.651
r_dihedral_angle_1_deg7.204
r_scangle_it4.948
r_scangle_other4.948
r_mcangle_other3.939
r_mcangle_it3.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.751
r_dihedral_angle_4_deg21.087
r_dihedral_angle_3_deg14.579
r_lrange_it8.651
r_lrange_other8.651
r_dihedral_angle_1_deg7.204
r_scangle_it4.948
r_scangle_other4.948
r_mcangle_other3.939
r_mcangle_it3.935
r_scbond_it3.2
r_scbond_other3.199
r_mcbond_it2.593
r_mcbond_other2.57
r_angle_refined_deg1.582
r_angle_other_deg1.273
r_symmetry_xyhbond_nbd_refined0.234
r_nbd_other0.217
r_nbd_refined0.201
r_symmetry_nbd_other0.184
r_symmetry_nbd_refined0.177
r_xyhbond_nbd_refined0.17
r_nbtor_refined0.168
r_symmetry_nbtor_other0.077
r_chiral_restr0.07
r_symmetry_xyhbond_nbd_other0.017
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3644
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing