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Substrate induced remodeling of the active site regulates HtrA1 activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LCY PDB ENTRY 1LCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 292 1.0M LiSO4, 0.1M sodium citrate pH5.6, 0.5M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.61 65.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.476 α = 90 b = 109.476 β = 90 c = 113.956 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2007-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.08090 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 50 95.7 0.395 20.6 3.3 12716 12716 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.75 2.85 85.5 0.395 1.6 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1LCY 2.75 19.32 12716 12062 628 95.74 0.24446 0.24243 0.2408 0.28747 0.2917 RANDOM 93.07
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.972 r_dihedral_angle_4_deg 22.658 r_dihedral_angle_3_deg 17.999 r_dihedral_angle_1_deg 6.984 r_scangle_it 2.457 r_angle_refined_deg 1.477 r_scbond_it 1.436 r_mcangle_it 1.059 r_angle_other_deg 0.898 r_mcbond_it 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.972 r_dihedral_angle_4_deg 22.658 r_dihedral_angle_3_deg 17.999 r_dihedral_angle_1_deg 6.984 r_scangle_it 2.457 r_angle_refined_deg 1.477 r_scbond_it 1.436 r_mcangle_it 1.059 r_angle_other_deg 0.898 r_mcbond_it 0.57 r_mcbond_other 0.103 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1407 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling