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Glycoside hydrolase BT_1012
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 40 % (v/v) MPD, 0.2 M ammonium phosphate and Tris pH
8.5
Crystal Properties Matthews coefficient Solvent content 3.79 67.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 262.455 α = 90 b = 262.455 β = 90 c = 184.883 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 38.95 99.5 10.8 10.7 106979
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 0.97 0.529 2.5 11
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 MOLECULAR REPLACEMENT THROUGHOUT 3KZS 2.3 38.95 101653 5323 99.43 0.1938 0.19199 0.1988 0.2283 0.2337 RANDOM 33.684
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] -0.12 -0.06 -0.12 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.683 r_dihedral_angle_3_deg 13.86 r_dihedral_angle_4_deg 12.652 r_dihedral_angle_1_deg 6.856 r_long_range_B_refined 5.261 r_long_range_B_other 5.228 r_scangle_other 3.789 r_mcangle_it 3.455 r_mcangle_other 3.455 r_scbond_it 2.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.683 r_dihedral_angle_3_deg 13.86 r_dihedral_angle_4_deg 12.652 r_dihedral_angle_1_deg 6.856 r_long_range_B_refined 5.261 r_long_range_B_other 5.228 r_scangle_other 3.789 r_mcangle_it 3.455 r_mcangle_other 3.455 r_scbond_it 2.412 r_scbond_other 2.345 r_mcbond_it 2.217 r_mcbond_other 2.217 r_angle_refined_deg 1.519 r_angle_other_deg 0.995 r_chiral_restr 0.092 r_bond_refined_d 0.013 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 11021 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 46
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement