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Structure of a beta galactosidase with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.285 α = 90.12 b = 115.735 β = 90 c = 115.981 γ = 90.03
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 PILATUS 6M-F 2017-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.5 115.98 96.5 0.049 0.998 11 3.5 798304
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 94.4 0.644 3.5
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 4D1I 1.5 115.98 758165 40094 96.48 0.1401 0.1379 0.1457 0.1817 0.1858 RANDOM 24.836
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] 0.03 -0.14 0.17 -0.23 -0.28 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 20.12 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 7.189 r_rigid_bond_restr 1.832 r_angle_refined_deg 1.444 r_angle_other_deg 1.41 r_chiral_restr 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 20.12 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 7.189 r_rigid_bond_restr 1.832 r_angle_refined_deg 1.444 r_angle_other_deg 1.41 r_chiral_restr 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33789 Nucleic Acid Atoms Solvent Atoms 4495 Heterogen Atoms 316
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling REFMAC phasing