☰ Navigation Tabs
Structure of invertase from Schwanniomyces occidentalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4W PDB ENTRY 1Y4W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 15% PEG 3350, 0.1M Hepes, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.71 66.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.778 α = 90 b = 119.49 β = 90 c = 137.677 γ = 90
Symmetry Space Group P 21 21 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 210 2008-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 2.8 59.76 99.7 0.197 0.197 9.7 6.9 43314
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 2.8 2.95 99.3 0.75 0.3 0.8 6.6 6197
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 1Y4W 2.9 59.65 37336 1980 99.74 0.22409 0.22236 0.2279 0.25716 0.2682 RANDOM 20.261
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] -0.12 -0.01 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_3_deg 19.254 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_1_deg 8.076 r_scangle_it 1.641 r_angle_refined_deg 1.453 r_scbond_it 0.895 r_mcangle_it 0.722 r_mcbond_it 0.378 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_3_deg 19.254 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_1_deg 8.076 r_scangle_it 1.641 r_angle_refined_deg 1.453 r_scbond_it 0.895 r_mcangle_it 0.722 r_mcbond_it 0.378 r_chiral_restr 0.126 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 8282 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 130
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction