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NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H75 PDB entry 1H75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.86 293 Na-citrate, Tris, MPD, spermidine, pH 7.86, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.63 α = 90 b = 89.63 β = 90 c = 40.15 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 IMAGE PLATE MARRESEARCH 2000-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.69 25 98.6 5187 5187
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.69 2.76 98.1
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1H75 2.69 23.7 5179 4942 237 98.31 0.24787 0.24513 0.24305 0.2436 0.2876 0.2875 RANDOM 30.383
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] 0.55 0.27 0.55 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.148 r_scangle_it 0.945 r_angle_refined_deg 0.894 r_angle_other_deg 0.694 r_mcangle_it 0.576 r_scbond_it 0.523 r_mcbond_it 0.311 r_symmetry_hbond_refined 0.307 r_symmetry_vdw_other 0.203 r_nbd_other 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.148 r_scangle_it 0.945 r_angle_refined_deg 0.894 r_angle_other_deg 0.694 r_mcangle_it 0.576 r_scbond_it 0.523 r_mcbond_it 0.311 r_symmetry_hbond_refined 0.307 r_symmetry_vdw_other 0.203 r_nbd_other 0.191 r_xyhbond_nbd_refined 0.183 r_nbd_refined 0.151 r_nbtor_other 0.083 r_symmetry_vdw_refined 0.08 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1150 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing