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Apoferritin: complex with 2,6-diethylphenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XZ1 pdb entry 1XZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Cadmium sulfate, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.13 60.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.456 α = 90 b = 181.456 β = 90 c = 181.456 γ = 90
Symmetry Space Group F 4 3 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 210 2007-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9537 NSLS X6A
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 1.68 32.08 97.9 0.099 13 14.83 29091 29091 2 30.5
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) 1.68 1.74 85.7 0.527 2 5.26 2484
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 FOURIER SYNTHESIS THROUGHOUT pdb entry 1XZ1 1.68 30.67 27587 1490 97.85 0.20007 0.19758 0.1991 0.2473 0.2488 RANDOM 30.866
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.719 r_dihedral_angle_4_deg 20.357 r_dihedral_angle_3_deg 13.891 r_scangle_it 4.638 r_dihedral_angle_1_deg 4.547 r_scbond_it 2.896 r_mcangle_it 1.716 r_angle_refined_deg 1.392 r_mcbond_it 0.945 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.719 r_dihedral_angle_4_deg 20.357 r_dihedral_angle_3_deg 13.891 r_scangle_it 4.638 r_dihedral_angle_1_deg 4.547 r_scbond_it 2.896 r_mcangle_it 1.716 r_angle_refined_deg 1.392 r_mcbond_it 0.945 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 1414 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing