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Crystal structure of Endoglucanase from Perinereis brevicirris
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 Bis-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 = 75.6 α = 90 b = 110.34 β = 90 c = 113.02 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 2014-07-09 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) 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 1.39 22.41 99.7 0.089 0.996 8.7 4.8 188755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.41 99.9 0.8 0.697 2.2 4.8 9282
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 1.39 22.41 179248 9289 99.58 0.1117 0.1098 0.1087 0.1479 0.1482 RANDOM 17.625
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] -0.8 2.72 -1.92
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.437 r_dihedral_angle_2_deg 37.292 r_sphericity_bonded 14.951 r_dihedral_angle_3_deg 12.59 r_dihedral_angle_4_deg 11.389 r_dihedral_angle_1_deg 5.627 r_rigid_bond_restr 2.654 r_mcangle_it 2.163 r_mcbond_it 1.869 r_mcbond_other 1.865
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.437 r_dihedral_angle_2_deg 37.292 r_sphericity_bonded 14.951 r_dihedral_angle_3_deg 12.59 r_dihedral_angle_4_deg 11.389 r_dihedral_angle_1_deg 5.627 r_rigid_bond_restr 2.654 r_mcangle_it 2.163 r_mcbond_it 1.869 r_mcbond_other 1.865 r_angle_refined_deg 1.702 r_angle_other_deg 1.067 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6603 Nucleic Acid Atoms Solvent Atoms 1078 Heterogen Atoms 51
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction