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Crystal structure of Leaf-branch compost bacterial cutinase homolog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% (w/v) polyethylene glycol (PEG) 3350, 200mM sodium thiocyanate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.911 α = 90 b = 71.084 β = 90 c = 72.726 γ = 90
Symmetry Space Group P 21 21 21
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 BRUKER SMART 6500 2011-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 50 99.9 0.106 0.106 31.657 13.7 35110 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 0.419 0.419 0.419 12.7 1742
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 1JFR 1.5 50 32818 1741 99.56 0.15801 0.15654 0.1599 0.1863 0.1884 RANDOM 17.172
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] -0.67 -0.04 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.304 r_dihedral_angle_4_deg 12.062 r_dihedral_angle_3_deg 10.84 r_dihedral_angle_1_deg 7.429 r_scangle_it 4.458 r_scbond_it 3.398 r_mcangle_it 2.175 r_mcbond_it 1.466 r_angle_refined_deg 1 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.304 r_dihedral_angle_4_deg 12.062 r_dihedral_angle_3_deg 10.84 r_dihedral_angle_1_deg 7.429 r_scangle_it 4.458 r_scbond_it 3.398 r_mcangle_it 2.175 r_mcbond_it 1.466 r_angle_refined_deg 1 r_chiral_restr 0.084 r_gen_planes_refined 0.02 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1962 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection