☰ Navigation Tabs
Structure of Apobacterioferritin Y25F variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VXI PDB ENTRY 2VXI
Crystallization Crystal Properties Matthews coefficient Solvent content 1.94 34.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.38 α = 90 b = 27.95 β = 119.37 c = 56.71 γ = 90
Symmetry Space Group C 1 2 1
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 CCD 2011-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.02 27.43 91.5 0.05 8.91 2.58 52678
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 1.1 1.13 57.2 0.41 1.74 1.69
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 2VXI 1.1 27.43 49990 2687 91.28 0.13534 0.13373 0.151 0.16544 0.1789 RANDOM 15.109
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] -0.08 -0.25 1.55 -0.73
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.154 r_dihedral_angle_2_deg 36.123 r_dihedral_angle_4_deg 16.055 r_sphericity_bonded 13.159 r_dihedral_angle_3_deg 12.147 r_rigid_bond_restr 6.457 r_dihedral_angle_1_deg 4.971 r_scbond_it 4.61 r_mcangle_it 3.208 r_mcbond_it 2.673
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.154 r_dihedral_angle_2_deg 36.123 r_dihedral_angle_4_deg 16.055 r_sphericity_bonded 13.159 r_dihedral_angle_3_deg 12.147 r_rigid_bond_restr 6.457 r_dihedral_angle_1_deg 4.971 r_scbond_it 4.61 r_mcangle_it 3.208 r_mcbond_it 2.673 r_mcbond_other 2.581 r_angle_refined_deg 1.967 r_angle_other_deg 0.933 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 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_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1286 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing