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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 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.416 α = 89.93 b = 115.786 β = 90.08 c = 116.186 γ = 89.99
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 2016-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 63.21 95.6 0.982 4.9 1.8 793061
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 0.585
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 63.21 752547 40511 94.54 0.1461 0.1451 0.1517 0.1644 0.1635 RANDOM 20.036
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] 3.83 -0.22 1.72 -4.61 3.39 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.099 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 13.917 r_dihedral_angle_1_deg 6.752 r_rigid_bond_restr 3.671 r_angle_refined_deg 1.837 r_angle_other_deg 1.566 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.099 r_dihedral_angle_4_deg 20.388 r_dihedral_angle_3_deg 13.917 r_dihedral_angle_1_deg 6.752 r_rigid_bond_restr 3.671 r_angle_refined_deg 1.837 r_angle_other_deg 1.566 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33088 Nucleic Acid Atoms Solvent Atoms 2095 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing