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Structure of the PDZ deleted variant of HtrA2 protease (S306A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 0.5 M Sodium acetate trihydrate pH 6.0, 2.0 M Sodium formate, 3% glycerol
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.88 α = 90 b = 82.88 β = 90 c = 395.31 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2020-12-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 4 40 90.7 0.967 4.36 4.24 11300 76.05
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 4 4.1 90.9 0.251 1.27 3.78
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LCY 4 39.53 11300 595 94.89 0.26859 0.26511 0.2636 0.33642 0.3384 RANDOM 108.477
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] -1.03 -1.03 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.144 r_dihedral_angle_3_deg 18.941 r_dihedral_angle_4_deg 12.932 r_dihedral_angle_1_deg 6.252 r_long_range_B_refined 5.614 r_long_range_B_other 5.614 r_mcangle_it 2.863 r_mcangle_other 2.863 r_scangle_other 2.262 r_mcbond_it 1.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.144 r_dihedral_angle_3_deg 18.941 r_dihedral_angle_4_deg 12.932 r_dihedral_angle_1_deg 6.252 r_long_range_B_refined 5.614 r_long_range_B_other 5.614 r_mcangle_it 2.863 r_mcangle_other 2.863 r_scangle_other 2.262 r_mcbond_it 1.687 r_mcbond_other 1.686 r_angle_refined_deg 1.497 r_scbond_it 1.222 r_scbond_other 1.222 r_angle_other_deg 1.186 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8149 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing