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Crystal structure of Endoglucanase from Perinereis brevicirris with Cellobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 100 mM Bris-Tris, pH5.5, 300 mM NaCl, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.15 α = 90 b = 108.17 β = 90 c = 112.68 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 PIXEL DECTRIS PILATUS 6M 2014-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.35 16.98 98 0.065 9.1 2.8 203725
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 97.1 0.532 2 2.9
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 3WC3 1.35 16.98 189171 9867 97.7 0.11665 0.11501 0.1142 0.14812 0.148 RANDOM 13.082
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] -0.45 0.46 -0.01
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.564 r_dihedral_angle_2_deg 36.579 r_dihedral_angle_4_deg 13.84 r_dihedral_angle_3_deg 12.501 r_sphericity_bonded 11.918 r_dihedral_angle_1_deg 5.617 r_long_range_B_refined 4.331 r_long_range_B_other 3.228 r_scangle_other 2.581 r_rigid_bond_restr 2.278
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.564 r_dihedral_angle_2_deg 36.579 r_dihedral_angle_4_deg 13.84 r_dihedral_angle_3_deg 12.501 r_sphericity_bonded 11.918 r_dihedral_angle_1_deg 5.617 r_long_range_B_refined 4.331 r_long_range_B_other 3.228 r_scangle_other 2.581 r_rigid_bond_restr 2.278 r_scbond_it 2.149 r_scbond_other 2.149 r_mcangle_other 1.778 r_mcangle_it 1.774 r_angle_refined_deg 1.61 r_mcbond_it 1.461 r_mcbond_other 1.449 r_angle_other_deg 1.023 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6598 Nucleic Acid Atoms Solvent Atoms 1118 Heterogen Atoms 54
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction