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The liganded structure of C. bescii family 3 pectate lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T9G PDB entry 3T9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1 M HEPES pH 7.5, 70% v/v (+/-)-2-Methyl 2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.946 α = 90 b = 35.898 β = 132 c = 98.687 γ = 90
Symmetry Space Group C 1 2 1
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 Platinum 135 HELIOS MIRRORS 2011-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 50 99.9 0.0584 13.62 4.83 47595 47595
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 100 0.3498 2.74 3.01 7847
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 PDB entry 3T9G 1.6 33.85 44501 2368 98.36 0.16584 0.16378 0.1703 0.20374 0.2068 RANDOM 18.436
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] -1.57 -1.51 1.3 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.375 r_dihedral_angle_4_deg 24.323 r_dihedral_angle_3_deg 12.52 r_dihedral_angle_1_deg 6.955 r_angle_refined_deg 2.175 r_angle_other_deg 1.104 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.375 r_dihedral_angle_4_deg 24.323 r_dihedral_angle_3_deg 12.52 r_dihedral_angle_1_deg 6.955 r_angle_refined_deg 2.175 r_angle_other_deg 1.104 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2954 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 136
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling