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nickel-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 sodium acetate, ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.331 α = 90 b = 64.331 β = 90 c = 32.12 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 1.9 100 91.5 0.074 9.7 1.9 3599 3599
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) 1.9 1.97 77.3 0.379 2.4 1.5 299
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1iro 2 20 3128 2996 132 100 0.21995 0.21888 0.24199 0.2832 RANDOM 25.528
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] -2.04 -1.02 -2.04 3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.214 r_scangle_it 1.691 r_angle_refined_deg 1.361 r_scbond_it 1.131 r_mcangle_it 0.93 r_angle_other_deg 0.863 r_mcbond_it 0.573 r_symmetry_vdw_other 0.25 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.214 r_scangle_it 1.691 r_angle_refined_deg 1.361 r_scbond_it 1.131 r_mcangle_it 0.93 r_angle_other_deg 0.863 r_mcbond_it 0.573 r_symmetry_vdw_other 0.25 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.225 r_nbd_other 0.225 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.095 r_nbtor_other 0.088 r_symmetry_hbond_refined 0.048 r_bond_refined_d 0.01 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 425 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling