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mercury-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 1.95 36.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.323 α = 90 b = 64.323 β = 90 c = 32.607 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 1.6 50 98.5 0.11 5.8 2.1 6532 6532
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) 1.6 1.66 90 0.271 2.4 1.7 591
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 1.6 16.07 6528 6223 305 100 0.15285 0.15112 0.171 0.18868 0.2084 RANDOM 12.193
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] -1.16 -0.58 -1.16 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.29 r_scangle_it 2.84 r_scbond_it 1.753 r_angle_refined_deg 1.275 r_mcangle_it 1.17 r_angle_other_deg 0.774 r_mcbond_it 0.627 r_symmetry_vdw_refined 0.247 r_nbd_other 0.232 r_symmetry_vdw_other 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.29 r_scangle_it 2.84 r_scbond_it 1.753 r_angle_refined_deg 1.275 r_mcangle_it 1.17 r_angle_other_deg 0.774 r_mcbond_it 0.627 r_symmetry_vdw_refined 0.247 r_nbd_other 0.232 r_symmetry_vdw_other 0.222 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.126 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.089 r_nbtor_other 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 422 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling