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Complex of equine apoferritin with the H-diaziflurane photolabeling reagent
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.05 M cadmium sulfate, 0.1 M HEPES, and 1.0 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.23 61.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.89 α = 90 b = 181.89 β = 90 c = 181.89 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 315 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9791 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 1.72 37.13 99 0.075 16.9 18.94 27676 27676
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 1.72 1.78 93 0.432 2.8 10.12 2547
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XZ1 1.72 37.13 27673 27673 1409 99.03 0.208 0.208 0.207 0.2061 0.217 0.2155 RANDOM 22.533
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 37.163 r_dihedral_angle_4_deg 21.931 r_dihedral_angle_3_deg 13.64 r_dihedral_angle_1_deg 4.577 r_scangle_it 4.262 r_scbond_it 2.596 r_mcbond_it 1.397 r_mcangle_it 1.395 r_angle_refined_deg 1.097 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.163 r_dihedral_angle_4_deg 21.931 r_dihedral_angle_3_deg 13.64 r_dihedral_angle_1_deg 4.577 r_scangle_it 4.262 r_scbond_it 2.596 r_mcbond_it 1.397 r_mcangle_it 1.395 r_angle_refined_deg 1.097 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.183 r_metal_ion_refined 0.133 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1354 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 17
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XTALVIEW refinement