☰ Navigation Tabs
Structure of Bradyrhizobium japonicum ScoI with copper bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1 M Na-citrate, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.86 α = 90 b = 44.76 β = 90 c = 40 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2014-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.4 46 91.2 0.099 0.103 17.04 12 30788 -3 19.097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.43 55.9 0.763 0.809 2.33
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 4txo 1.4 42 30788 1494 91.2 0.1283 0.126 0.1259 0.1753 0.1759 RANDOM 18.926
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] 0.47 -0.27 -0.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.923 r_dihedral_angle_2_deg 33.436 r_dihedral_angle_4_deg 18.667 r_sphericity_bonded 14.632 r_dihedral_angle_3_deg 13.459 r_dihedral_angle_1_deg 5.793 r_rigid_bond_restr 5.405 r_mcangle_it 3.779 r_mcbond_it 3.729 r_mcbond_other 3.721
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 49.923 r_dihedral_angle_2_deg 33.436 r_dihedral_angle_4_deg 18.667 r_sphericity_bonded 14.632 r_dihedral_angle_3_deg 13.459 r_dihedral_angle_1_deg 5.793 r_rigid_bond_restr 5.405 r_mcangle_it 3.779 r_mcbond_it 3.729 r_mcbond_other 3.721 r_angle_refined_deg 2.012 r_angle_other_deg 0.989 r_chiral_restr 0.146 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing XSCALE data reduction