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Structure of CBM35 in complex with glucuronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QB1 PDB ENTRY 4QB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% PEG 6000, 0.2M Calcium chloride, 0.1M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.891 α = 90 b = 47.552 β = 90 c = 102.735 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 120 PIXEL DECTRIS PILATUS 6M-F 2014-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.978583 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 102.74 99.6 0.097 0.028 16 12.9 414192 32026 1 1 9.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 100 0.51 0.146 5.1 13 4619
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 4QB1 1.5 51.37 1 1 414192 30348 1618 99.55 0.15569 0.15499 0.1563 0.16882 0.1696 RANDOM 14.625
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] -0.07 0.86 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.124 r_dihedral_angle_4_deg 18.933 r_dihedral_angle_3_deg 12.155 r_dihedral_angle_1_deg 7.24 r_long_range_B_refined 4.436 r_long_range_B_other 4.272 r_scangle_other 3.198 r_scbond_it 2.272 r_scbond_other 2.247 r_mcangle_other 2.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.124 r_dihedral_angle_4_deg 18.933 r_dihedral_angle_3_deg 12.155 r_dihedral_angle_1_deg 7.24 r_long_range_B_refined 4.436 r_long_range_B_other 4.272 r_scangle_other 3.198 r_scbond_it 2.272 r_scbond_other 2.247 r_mcangle_other 2.185 r_mcangle_it 2.179 r_angle_refined_deg 1.84 r_mcbond_it 1.372 r_mcbond_other 1.356 r_angle_other_deg 0.905 r_chiral_restr 0.117 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 981 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 28
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling