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Crystal structure of human beta-galactosidase mutant I51T in complex with 6S-NBI-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, pH 7.5, vapor diffusion, sittingdrop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.026 α = 90 b = 116.175 β = 92.29 c = 140.68 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 2013-01-20 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 99.1 0.173 11.5 3.8 134623
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 2.34 100 0.677 2.3 3.7
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 25.14 127821 6756 99.11 0.18239 0.17936 0.1857 0.23975 0.2385 RANDOM 28.964
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 37.493 r_dihedral_angle_4_deg 20.012 r_dihedral_angle_3_deg 15.669 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 1.855 r_angle_other_deg 1.505 r_chiral_restr 0.114 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 37.493 r_dihedral_angle_4_deg 20.012 r_dihedral_angle_3_deg 15.669 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 1.855 r_angle_other_deg 1.505 r_chiral_restr 0.114 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 19202 Nucleic Acid Atoms Solvent Atoms 1241 Heterogen Atoms 368
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