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The unliganded structure of Caldicellulosiruptor saccharolyticus GH5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G01
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.0 M sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.66 α = 90 b = 146.66 β = 90 c = 146.66 γ = 90
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 2012-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
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 1.5 20 100 0.095 42.5 59 83455
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 1.5 1.54 100 0.887 6 40
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 1G01 1.5 19.96 79213 4144 99.83 0.08651 0.08503 0.0863 0.11477 0.1156 RANDOM 18.801
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.888 r_sphericity_bonded 20.579 r_dihedral_angle_4_deg 18.909 r_sphericity_free 16.867 r_dihedral_angle_3_deg 12.159 r_scbond_it 9.622 r_scbond_other 9.619 r_rigid_bond_restr 9.166 r_scangle_other 7.742 r_long_range_B_refined 6.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.888 r_sphericity_bonded 20.579 r_dihedral_angle_4_deg 18.909 r_sphericity_free 16.867 r_dihedral_angle_3_deg 12.159 r_scbond_it 9.622 r_scbond_other 9.619 r_rigid_bond_restr 9.166 r_scangle_other 7.742 r_long_range_B_refined 6.999 r_long_range_B_other 6.802 r_dihedral_angle_1_deg 6.766 r_angle_refined_deg 2.681 r_mcangle_it 2.314 r_mcangle_other 2.314 r_mcbond_it 2.06 r_mcbond_other 2.015 r_angle_other_deg 1.288 r_chiral_restr 0.173 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_gen_planes_other 0.004 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2774 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Blu-Ice data collection MOLREP phasing