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cobalt-substituted rubredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 37.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.247 α = 90 b = 64.247 β = 90 c = 32.854 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 298 IMAGE PLATE RIGAKU RAXIS IIC mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 50 99.7 0.064 11.6 2.3 5552 5552
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 99.8 0.393 2.3 2.2 565
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 (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 1iro 1.7 20 5524 5276 248 100 0.14722 0.14498 0.164 0.19676 0.2109 RANDOM 20.57
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] -1.19 -0.59 -1.19 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.323 r_scangle_it 3.549 r_scbond_it 2.2 r_mcangle_it 1.44 r_angle_refined_deg 1.409 r_angle_other_deg 0.857 r_mcbond_it 0.745 r_nbd_other 0.245 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.323 r_scangle_it 3.549 r_scbond_it 2.2 r_mcangle_it 1.44 r_angle_refined_deg 1.409 r_angle_other_deg 0.857 r_mcbond_it 0.745 r_nbd_other 0.245 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.231 r_symmetry_vdw_other 0.22 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.146 r_nbtor_other 0.094 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 421 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling