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Structure of Caldicellulosiruptor danielii GH10 module of glycoside hydrolase WP_045175321
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AY7 PDB entry 5AY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Tris, pH 8-9, 1.5-2.1 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.307 α = 90 b = 98.497 β = 93.58 c = 78.81 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 2016-05-31 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 1.9 50 100 0.068 14.32 6.03 104001
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 1.9 2 100 0.4469 2.11 3.54
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 5AY7 1.9 86.48 98265 5058 99.3 0.18147 0.17882 0.1869 0.23331 0.2402 RANDOM 27.186
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] 0.44 -0.92 -1.51 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.091 r_dihedral_angle_4_deg 16.435 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 6.141 r_long_range_B_other 6.141 r_scangle_other 4.459 r_scbond_it 3.117 r_scbond_other 3.114 r_mcangle_it 3.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.091 r_dihedral_angle_4_deg 16.435 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 6.141 r_long_range_B_other 6.141 r_scangle_other 4.459 r_scbond_it 3.117 r_scbond_other 3.114 r_mcangle_it 3.096 r_mcangle_other 3.096 r_mcbond_it 2.363 r_mcbond_other 2.363 r_angle_refined_deg 1.804 r_angle_other_deg 1.075 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8280 Nucleic Acid Atoms Solvent Atoms 1281 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement SAINT data reduction PROTEUM PLUS data scaling MOLREP phasing