☰ Navigation Tabs
Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X34 PDB ENTRY 2X34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.378 α = 90 b = 64.36 β = 90 c = 84.732 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 120 CCD ADSC QUANTUM 4r 2008-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.55 35 100 0.06 17.1 5.9 51047 1.5 14.3
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) 1 1.55 1.63 100 0.48 3.3 6
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 2X34 1.55 51.23 48401 2584 99.96 0.16028 0.1585 0.1783 0.19418 0.2093 RANDOM 7.379
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] -0.7 0.16 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.322 r_dihedral_angle_4_deg 12.917 r_dihedral_angle_3_deg 11.984 r_dihedral_angle_1_deg 6.03 r_scangle_it 3.77 r_scbond_it 2.612 r_angle_refined_deg 1.872 r_mcangle_it 1.786 r_mcbond_it 1.062 r_angle_other_deg 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.322 r_dihedral_angle_4_deg 12.917 r_dihedral_angle_3_deg 11.984 r_dihedral_angle_1_deg 6.03 r_scangle_it 3.77 r_scbond_it 2.612 r_angle_refined_deg 1.872 r_mcangle_it 1.786 r_mcbond_it 1.062 r_angle_other_deg 1.01 r_mcbond_other 0.331 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2630 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing