☰ Navigation Tabs
Granule Bound Starch Synthase I from Cyanophora paradoxa bound to acarbose and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VUE 3vue, 2qzs experimental model PDB 2QZS 3vue, 2qzs
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 288 40 mM citric acid, 60 mM bis-tris propane pH 6.4 and 20% PEG 3350, 0.025 M chromium chloride, acarbose, ADP
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.3 α = 90 b = 106.1 β = 90 c = 175.5 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 PIXEL DECTRIS PILATUS3 2M 2012-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.9 200 90.8 0.371 0.968 4.59 3.5 26755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 92.6 2.49 0.429 0.72 3.4
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 3vue, 2qzs 2.95 20 24587 760 90.51 0.27344 0.27248 0.2855 0.30293 0.3142 RANDOM 62.378
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] -5.18 11.62 -6.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_3_deg 19.611 r_dihedral_angle_4_deg 17.408 r_long_range_B_refined 8.822 r_long_range_B_other 8.822 r_dihedral_angle_1_deg 7.289 r_mcangle_it 3.984 r_mcangle_other 3.984 r_scangle_other 3.532 r_mcbond_it 2.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_3_deg 19.611 r_dihedral_angle_4_deg 17.408 r_long_range_B_refined 8.822 r_long_range_B_other 8.822 r_dihedral_angle_1_deg 7.289 r_mcangle_it 3.984 r_mcangle_other 3.984 r_scangle_other 3.532 r_mcbond_it 2.331 r_mcbond_other 2.331 r_scbond_it 2.011 r_scbond_other 2.011 r_angle_refined_deg 1.464 r_angle_other_deg 1.008 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8107 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing