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X-ray structure of the (hydro)peroxo intermediate NikA/1-Int", after monohydroxylation of the iron complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZLQ PDB ENTRY 1ZLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 293 1.8M ammonium acetate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.727 α = 90 b = 94.298 β = 90 c = 124.557 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 210 2009-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 47.2 93 0.063 11.2 2.7 105943 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 93 0.293 3.4 2.5 29711
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 1ZLQ 1.7 47.15 105943 5576 100 0.16581 0.16398 0.1664 0.2004 0.1994 RANDOM 17.236
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] -0.2 -0.5 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.683 r_dihedral_angle_4_deg 15.29 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.096 r_scangle_it 3.446 r_scbond_it 2.132 r_angle_refined_deg 1.391 r_mcangle_it 1.361 r_mcbond_it 0.846 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.683 r_dihedral_angle_4_deg 15.29 r_dihedral_angle_3_deg 13.423 r_dihedral_angle_1_deg 6.096 r_scangle_it 3.446 r_scbond_it 2.132 r_angle_refined_deg 1.391 r_mcangle_it 1.361 r_mcbond_it 0.846 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7884 Nucleic Acid Atoms Solvent Atoms 1089 Heterogen Atoms 193
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling