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The crystal structure of the D73A mutant of glycoside HYDROLASE (FAMILY 31) from Ruminococcus obeum ATCC 29174
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FFJ PDB entry 3FFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.1M BIS-TRIS, 25% PEG3350, 5mM maltose, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.182 α = 90 b = 122.486 β = 108.6 c = 87.46 γ = 90
Symmetry Space Group P 1 21 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 315r Mirror 2010-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97951 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.65 83 99.5 0.143 8.8 3.5 36534 36534
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 99.2 0.742 1.45 3.4 2001
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3FFJ 2.66 82.89 34687 34687 1825 99.03 0.1922 0.1922 0.18874 0.1892 0.25788 0.2581 RANDOM 37.13
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] -0.95 -0.41 1.9 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_3_deg 19.8 r_dihedral_angle_4_deg 18.227 r_dihedral_angle_1_deg 6.81 r_scangle_it 3.168 r_scbond_it 1.917 r_angle_refined_deg 1.535 r_mcangle_it 1.239 r_mcbond_it 0.628 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_3_deg 19.8 r_dihedral_angle_4_deg 18.227 r_dihedral_angle_1_deg 6.81 r_scangle_it 3.168 r_scbond_it 1.917 r_angle_refined_deg 1.535 r_mcangle_it 1.239 r_mcbond_it 0.628 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10654 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 6
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling