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Crystal structure of Alpha-galactosidase (EC 3.2.1.22) (Melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 8.3 273 0.2M K3Cirtrate, 20.0% PEG-3350, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 3.4 63.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.729 α = 90 b = 160.533 β = 90 c = 88.258 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Flat mirror, Side-defelecting monochromator (Si 111) 2005-05-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979413, 0.918370, 0.979170 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.34 42.88 98 0.129 0.129 5.7 3.7 35967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.47 99.4 0.603 0.603 1.3 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.34 42.504 34093 1792 97.41 0.165 0.162 0.1708 0.213 0.2174 RANDOM 27.55
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] 0.38 1.61 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_4_deg 17.758 r_dihedral_angle_3_deg 15.633 r_scangle_it 7.69 r_dihedral_angle_1_deg 7.102 r_scbond_it 5.917 r_mcangle_it 3.324 r_mcbond_it 2.588 r_angle_refined_deg 1.55 r_angle_other_deg 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_4_deg 17.758 r_dihedral_angle_3_deg 15.633 r_scangle_it 7.69 r_dihedral_angle_1_deg 7.102 r_scbond_it 5.917 r_mcangle_it 3.324 r_mcbond_it 2.588 r_angle_refined_deg 1.55 r_angle_other_deg 0.812 r_mcbond_other 0.508 r_nbd_refined 0.193 r_nbd_other 0.184 r_nbtor_refined 0.183 r_symmetry_vdw_other 0.175 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.137 r_symmetry_vdw_refined 0.108 r_chiral_restr 0.089 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4232 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing