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Crystal structure of human beta-galactosidase in complex with NBT-DGJ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3THC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 PEG 3350, Ammonium sulfate, HEPES, pH 7.5, vapor diffusion, sittingdrop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.119 α = 90 b = 116.26 β = 92.41 c = 141.768 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2013-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 50 98.3 0.171 13.5 4.5 133461
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 98.6 0.763 2.5 4.5
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 3THC 2.3 25.98 126692 6716 97.43 0.17789 0.17459 0.1823 0.24047 0.2425 RANDOM 31.906
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.593 r_dihedral_angle_4_deg 20.265 r_dihedral_angle_3_deg 16.048 r_dihedral_angle_1_deg 7.322 r_angle_refined_deg 1.803 r_angle_other_deg 1.197 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.593 r_dihedral_angle_4_deg 20.265 r_dihedral_angle_3_deg 16.048 r_dihedral_angle_1_deg 7.322 r_angle_refined_deg 1.803 r_angle_other_deg 1.197 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19206 Nucleic Acid Atoms Solvent Atoms 1092 Heterogen Atoms 372
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing