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Crystal structure of the GH12 domain from Acidothermus cellulolyticus GuxA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B7M PDB entry 3B7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 10% PEG8000, 0.2 M zinc chloride, 0.1 M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 3.15 60.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.182 α = 90 b = 66.182 β = 90 c = 127.893 γ = 120
Symmetry Space Group P 31 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 2008-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM 1.54178
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 1.5 27.98 99.7 0.052 0.997 10.3 1.9 52722
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 1.5 1.53 97.4 0.329 0.654 2.2 1.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3B7M 1.5 27.98 52550 2663 99.676 0.131 0.1291 0.1295 0.1711 0.1709 11.627
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] -0.096 -0.048 -0.096 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_dihedral_angle_4_deg 28.096 r_dihedral_angle_1_deg 18.244 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_other_3_deg 10.433 r_lrange_it 5.406 r_lrange_other 5.405 r_rigid_bond_restr 3.361 r_scangle_it 2.814 r_scangle_other 2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_dihedral_angle_4_deg 28.096 r_dihedral_angle_1_deg 18.244 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_other_3_deg 10.433 r_lrange_it 5.406 r_lrange_other 5.405 r_rigid_bond_restr 3.361 r_scangle_it 2.814 r_scangle_other 2.814 r_mcangle_it 2.591 r_mcangle_other 2.591 r_scbond_it 2.5 r_scbond_other 2.499 r_angle_refined_deg 2.049 r_mcbond_it 1.908 r_mcbond_other 1.898 r_angle_other_deg 1.657 r_metal_ion_refined 0.319 r_symmetry_xyhbond_nbd_refined 0.306 r_nbd_other 0.283 r_xyhbond_nbd_refined 0.261 r_nbd_refined 0.245 r_symmetry_nbd_other 0.212 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.172 r_symmetry_metal_ion_refined 0.123 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1773 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing