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ENDO-POLYGALACTURONASE FROM ARABIDOPSIS THALIANA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 0.2 M Sodium fluoride, 0.1 M Bis-Tris propane pH 8.5, 20 % w/v PEG 3350 (H1 condition, PACT premier plate)
Crystal Properties Matthews coefficient Solvent content 1.89 37.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.97 α = 93.25 b = 41.83 β = 99.86 c = 63.33 γ = 114.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100.15 PIXEL DECTRIS PILATUS3 6M 2018-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.3 34.5 96.16 0.076 0.026 0.999 16.2 9.1 83670 14.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 92.1 0.777 0.32 0.864
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1RMG 1.3 34.5 1.96 83634 4182 96.13 0.1437 0.1419 0.1445 0.1774 0.1778 29.31
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.7614 f_angle_d 1.5309 f_chiral_restr 0.1109 f_bond_d 0.0123 f_plane_restr 0.0113
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2909 Nucleic Acid Atoms Solvent Atoms 607 Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement PHASER phasing XSCALE data scaling Aimless data reduction