☰ Navigation Tabs
Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2M Sodium acetate, 0.1M Sodium cacodylate, 1mM Calcium chloride, 30% w/v Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 1.862 33.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.886 α = 103.78 b = 43.517 β = 92.42 c = 51.724 γ = 101.49
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 2010-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.27 36.72 89.5 0.075 0.087 0.044 0.998 13.3 3.9 68333
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.29 82.3 0.44 0.515 0.266 0.819 3.7
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 1CEX 1.27 36.69 64992 3328 89.57 0.1265 0.1239 0.1244 0.1768 0.1767 RANDOM 8.595
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] 0.13 0.2 0.05 -0.31 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_3_deg 12.255 r_dihedral_angle_1_deg 6.316 r_rigid_bond_restr 2.811 r_angle_refined_deg 1.989 r_angle_other_deg 1.706 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_3_deg 12.255 r_dihedral_angle_1_deg 6.316 r_rigid_bond_restr 2.811 r_angle_refined_deg 1.989 r_angle_other_deg 1.706 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2787 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing