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Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D9Y PDB ENTRY 1D9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 290 4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40
Crystal Properties Matthews coefficient Solvent content 1.94 36.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.128 α = 90 b = 148.128 β = 90 c = 115.842 γ = 120
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 MIRRORS 2001-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.6 30 100 0.08 7.4 8.4 406392 28.5
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 1.6 1.63 100 0.584 1.8 5.8
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 1D9Y 1.65 30 341561 23837 100 0.1642 0.1642 0.1651 0.2624 0.2305 RANDOM 31.2
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] -3.474 -3.028 -3.474 6.949
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.2 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.2 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21393 Nucleic Acid Atoms Solvent Atoms 1976 Heterogen Atoms 236
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS phasing CNS refinement