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Crystal structure of alpha-galactosidase I from Mortierella vinacea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UAS PDB ENTRY 1UAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M trisodium citrate dihydrate, 0.1M Tris buffer pH 8.5, 30% polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.77 67.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.47 α = 90 b = 142.47 β = 90 c = 130.58 γ = 90
Symmetry Space Group I 4 2 2
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 MARRESEARCH 2004-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0313 SPring-8 BL41XU
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 50 99.9 0.09 0.084 8.4 7.7 45399
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 2.11 99.9 0.343 0.314 2.4 6.1 6533
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 PDB ENTRY 1UAS 2 24.16 45392 2291 99.96 0.1433 0.14186 0.1437 0.17008 0.1712 RANDOM 18.994
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 38.627 r_dihedral_angle_3_deg 12.03 r_dihedral_angle_4_deg 11.122 r_dihedral_angle_1_deg 6.547 r_scangle_it 2.957 r_scbond_it 1.826 r_angle_refined_deg 1.291 r_mcangle_it 1.067 r_mcbond_it 0.66 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.627 r_dihedral_angle_3_deg 12.03 r_dihedral_angle_4_deg 11.122 r_dihedral_angle_1_deg 6.547 r_scangle_it 2.957 r_scbond_it 1.826 r_angle_refined_deg 1.291 r_mcangle_it 1.067 r_mcbond_it 0.66 r_nbtor_refined 0.304 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.18 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3087 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 213
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DPS data reduction SCALA data scaling