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HIT family hydrolase from Clostridium thermocellum Cth-393
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% w/v PEG 3000, 0.2M sodium chloride, 0.1M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.804 α = 90 b = 78.804 β = 90 c = 114.885 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.969 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 20 98 16265
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 FOURIER SYNTHESIS FREE R-VALUE 1XQU 2.3 20 15683 495 97.17 0.20678 0.20597 0.2184 0.23292 0.2506 FLAGS TAKEN FROM PDB ENTRY 1XQU 40.717
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 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.798 r_dihedral_angle_4_deg 16.331 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 7.059 r_long_range_B_refined 6.566 r_long_range_B_other 6.561 r_scangle_other 5.014 r_mcangle_other 4.356 r_mcangle_it 4.354 r_scbond_it 3.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.798 r_dihedral_angle_4_deg 16.331 r_dihedral_angle_3_deg 13.255 r_dihedral_angle_1_deg 7.059 r_long_range_B_refined 6.566 r_long_range_B_other 6.561 r_scangle_other 5.014 r_mcangle_other 4.356 r_mcangle_it 4.354 r_scbond_it 3.259 r_scbond_other 3.257 r_mcbond_it 2.939 r_mcbond_other 2.932 r_angle_refined_deg 1.765 r_angle_other_deg 1.046 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 1742 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing