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X/N joint refinement of Achromobacter Lyticus Protease I free form at pD8.0
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ARC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 297 20% w/v PEG 3350, 10mM Tris, HCl pH 8.0, 50% PEG 3350, HCl pD 8.0, VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.1 41.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.574 α = 64.82 b = 40.785 β = 66.1 c = 43.98 γ = 73.42
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 297 IMAGE PLATE BIX-4, SILICON 2007-06-12 M SINGLE WAVELENGTH 2 1 x-ray 297 IMAGE PLATE MAC Science DIP-2000 double mirror 2007-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR JRR-3M BEAMLINE 1G-C 2.6 JRR-3M 1G-C 2 ROTATING ANODE MACSCIENCE M06X 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.98 50 89.4 0.161 4.87 11000 2 1.895 50 89.4 0.078 17.38 16128
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 1.88 1.95 0.198 5.95 2 1.95 2.03 0.17 7.2 2 2.03 2.12 0.135 9.3 2 2.12 2.23 0.121 10.5 2 2.23 2.37 0.112 11.6 2 2.37 2.55 0.099 13 2 2.55 2.81 0.086 15.3 2 2.81 3.21 0.075 17.8 2 3.21 4.05 0.062 23 2 4.05 80 0.062 23.3 2 2 2.07 0.319 2.5 2 2.07 2.15 0.342 2.9 2 2.15 2.25 0.33 3.2 2 2.25 2.37 0.329 2.9 2 2.37 2.52 0.288 3.3 2 2.52 2.71 0.289 3.7 2 2.71 2.99 0.247 4.5 2 2.99 3.42 0.18 6.7 2 3.42 4.31 0.139 9.7 2 4.31 50 0.124 10.7 1 2 2.07 0.319 2.51
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.895 20.358 2.08 16081 800 89.99 0.1493 0.1466 0.1526 0.2028 0.2077 NEUTRON DIFFRACTION 1.979 37.61 10998 554 69.97 0.1984 0.1952 0.2595
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] -2.3375 1.7676 2.5966 4.4118 -2.9931 -2.0743 -0.058 -1.3327 0.8508 -1.2985 0.8387 -3.4569
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.315 f_angle_d 1.473 f_chiral_restr 0.096 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1920 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms
Software Software Software Name Purpose MacScience data collection PHENIX refinement DENZO data reduction SCALEPACK data scaling