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Crystal structure of Caldicellulosiruptor saccharolyticus CBM27-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PMH PDB entry 1PMH, CBM27-1 in complex with mannohexaose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283.15 Peg 4000, Isopropanol, Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283.15K
Crystal Properties Matthews coefficient Solvent content 2.1 41.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.988 α = 90 b = 54.988 β = 90 c = 115.777 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH mirrors 2003-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.97626 BESSY 14.2
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 1.55 24.6 98.6 0.051 13.6 4.1 26236 15.8
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) 1.55 1.59 98.3 0.372 1708
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1PMH, CBM27-1 in complex with mannohexaose 1.55 24.6 2 26208 24319 1889 98.74 0.172 0.12779 0.12427 0.1271 0.17388 0.1786 RANDOM 13.456
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] -0.5 -0.5 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.767 r_scangle_it 5.169 r_sphericity_free 4.537 r_scbond_it 3.612 r_sphericity_bonded 3.612 r_mcangle_it 3.266 r_mcbond_it 2.414 r_rigid_bond_restr 2.122 r_angle_refined_deg 1.544 r_angle_other_deg 0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.767 r_scangle_it 5.169 r_sphericity_free 4.537 r_scbond_it 3.612 r_sphericity_bonded 3.612 r_mcangle_it 3.266 r_mcbond_it 2.414 r_rigid_bond_restr 2.122 r_angle_refined_deg 1.544 r_angle_other_deg 0.849 r_nbd_other 0.262 r_symmetry_vdw_other 0.244 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.103 r_nbtor_other 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1508 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing