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Apoferritin: complex with phenol
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 3.14 60.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.532 α = 90 b = 181.532 β = 90 c = 181.532 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 2006-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9795 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 1.7 20.97 99.4 0.072 17.1 17.75 28612 28612 3.1 37.07
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) 1.7 1.76 96.4 0.46 3.1 8.27 2739
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 1XZ1 1.85 20.97 21259 1147 99.88 0.18546 0.18386 0.21602 0.2151 RANDOM 26.963
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 35.607 r_dihedral_angle_4_deg 21.008 r_dihedral_angle_3_deg 13.918 r_scangle_it 5.724 r_dihedral_angle_1_deg 4.798 r_scbond_it 3.369 r_mcangle_it 1.88 r_angle_refined_deg 1.396 r_mcbond_it 0.962 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.607 r_dihedral_angle_4_deg 21.008 r_dihedral_angle_3_deg 13.918 r_scangle_it 5.724 r_dihedral_angle_1_deg 4.798 r_scbond_it 3.369 r_mcangle_it 1.88 r_angle_refined_deg 1.396 r_mcbond_it 0.962 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 1399 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing