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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 54.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.12 α = 90.2 b = 115.91 β = 89.96 c = 116.103 γ = 90.08
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 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) 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 1.46 116.1 96.4 0.996 9.6 3.4 865389
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 1.46 1.48 0.662
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 1.46 116.1 821933 43369 96.35 0.1282 0.1259 0.1349 0.1718 0.1762 RANDOM 22.723
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] 0.31 0.63 -0.4 -1.36 -0.61 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_4_deg 20.005 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 7.25 r_rigid_bond_restr 5.156 r_angle_refined_deg 1.979 r_angle_other_deg 1.608 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_4_deg 20.005 r_dihedral_angle_3_deg 11.998 r_dihedral_angle_1_deg 7.25 r_rigid_bond_restr 5.156 r_angle_refined_deg 1.979 r_angle_other_deg 1.608 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33818 Nucleic Acid Atoms Solvent Atoms 5125 Heterogen Atoms 256
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling REFMAC phasing