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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 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.952 α = 89.84 b = 116.052 β = 90.07 c = 115.576 γ = 89.98
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 0.9795 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 1.6 63.2 95.8 0.995 4.6 2.1 650269
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 1.6 1.63 0.678
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 1.6 63.2 617754 32511 95.78 0.1549 0.1519 0.163 0.2118 0.2186 RANDOM 26.906
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] 0.22 -0.04 -1.4 -1.16 -0.02 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.665 r_dihedral_angle_4_deg 20.806 r_dihedral_angle_3_deg 13.993 r_rigid_bond_restr 7.169 r_dihedral_angle_1_deg 6.551 r_angle_refined_deg 1.942 r_angle_other_deg 1.684 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.665 r_dihedral_angle_4_deg 20.806 r_dihedral_angle_3_deg 13.993 r_rigid_bond_restr 7.169 r_dihedral_angle_1_deg 6.551 r_angle_refined_deg 1.942 r_angle_other_deg 1.684 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.011 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33342 Nucleic Acid Atoms Solvent Atoms 2502 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling REFMAC phasing