☰ Navigation Tabs
Crystal structures of Cupin superfamily BbDUF985 from Branchiostoma belcheri tsingtauense in apo and GDP-bound forms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 289 2.0M ammonium sulfate, 0.1M sodium acetate trihydate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal Properties Matthews coefficient Solvent content 4.24 71.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.86 α = 90 b = 88.86 β = 90 c = 168.17 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2009-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.5 84.22 98.6 0.053 15.6 2.7 22168 56.3
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) 2.5 2.64 98.9 0.371 3.1 2.7 3223
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 1YUD 2.5 19.94 20964 1125 98.12 0.20054 0.19835 0.2039 0.24125 0.2438 RANDOM 35.993
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] 1.12 1.12 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.083 r_dihedral_angle_3_deg 16.887 r_dihedral_angle_4_deg 15.773 r_dihedral_angle_1_deg 7.389 r_scangle_it 5.836 r_scbond_it 3.561 r_mcangle_it 2.233 r_angle_refined_deg 2.067 r_mcbond_it 1.149 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.083 r_dihedral_angle_3_deg 16.887 r_dihedral_angle_4_deg 15.773 r_dihedral_angle_1_deg 7.389 r_scangle_it 5.836 r_scbond_it 3.561 r_mcangle_it 2.233 r_angle_refined_deg 2.067 r_mcbond_it 1.149 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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 2588 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 64
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling