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Crystal structure of bacterioferritin from R.sphaeroides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JGC PDB ENTRY 1JGC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 0.1M Na-citrate, pH5.6, 14-20% (w/v) PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.36 63.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.495 α = 90 b = 160.495 β = 90 c = 116.276 γ = 90
Symmetry Space Group I 4 2 2
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 QUANTUM 315 2009-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.000 PAL/PLS 4A
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 2.8 50 89.4 0.142 0.142 9.4 5.2 17331
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) 2.8 2.9 81.4 0.357 2.9 1543
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 1JGC 2.8 41.57 16139 866 89.52 0.2295 0.22674 0.2235 0.2844 0.281 RANDOM 24.253
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] -0.02 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.296 r_dihedral_angle_3_deg 19.74 r_dihedral_angle_4_deg 17.742 r_dihedral_angle_1_deg 5.498 r_scangle_it 3.842 r_scbond_it 2.279 r_angle_refined_deg 1.72 r_mcangle_it 1.371 r_mcbond_it 0.659 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.296 r_dihedral_angle_3_deg 19.74 r_dihedral_angle_4_deg 17.742 r_dihedral_angle_1_deg 5.498 r_scangle_it 3.842 r_scbond_it 2.279 r_angle_refined_deg 1.72 r_mcangle_it 1.371 r_mcbond_it 0.659 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 3832 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 89
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction REFMAC refinement