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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 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.103 α = 90.21 b = 115.386 β = 89.99 c = 115.723 γ = 89.85
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 2M 2018-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 82 96.2 0.986 5.9 2.2 789757
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 0.604
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 81.86 749920 39666 96.12 0.1337 0.1311 0.1409 0.1822 0.1865 RANDOM 22.626
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] -0.14 0.49 -0.68 0.04 -0.47 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.306 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 12.441 r_dihedral_angle_1_deg 7.074 r_rigid_bond_restr 5.137 r_angle_refined_deg 1.96 r_angle_other_deg 1.62 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.306 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 12.441 r_dihedral_angle_1_deg 7.074 r_rigid_bond_restr 5.137 r_angle_refined_deg 1.96 r_angle_other_deg 1.62 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33712 Nucleic Acid Atoms Solvent Atoms 3978 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing