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Crystal structure of CBM42A from Clostridium thermocellum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WD3 PDB ENTRY 1WD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1M sodium acetate, 2.1M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.37 α = 90 b = 106.37 β = 90 c = 237.564 γ = 120
Symmetry Space Group P 32 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 ADSC QUANTUM 315 mirror 2007-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.8 237.564 99.9 0.089 0.089 19.8 9.8 144547 2 2
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 1.8 1.9 99.8 0.381 0.381 2 9.2 20870
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WD3 1.8 45.22 144449 7239 99.92 0.192 0.16 0.158 0.192 0.2317 RANDOM 9.877
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.474 r_dihedral_angle_4_deg 14.762 r_dihedral_angle_3_deg 13.15 r_dihedral_angle_1_deg 7.319 r_scangle_it 4.832 r_scbond_it 3.233 r_angle_refined_deg 2.121 r_mcangle_it 2.019 r_mcbond_it 1.293 r_chiral_restr 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.474 r_dihedral_angle_4_deg 14.762 r_dihedral_angle_3_deg 13.15 r_dihedral_angle_1_deg 7.319 r_scangle_it 4.832 r_scbond_it 3.233 r_angle_refined_deg 2.121 r_mcangle_it 2.019 r_mcbond_it 1.293 r_chiral_restr 0.191 r_bond_refined_d 0.028 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9058 Nucleic Acid Atoms Solvent Atoms 863 Heterogen Atoms 105
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection