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X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 293 1.8M ammonium sulfate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.04 α = 90 b = 93.873 β = 90 c = 124.726 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 315r 2008-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.96850 ESRF ID14-4
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 46.93 96 0.058 16.42 5.4 108346 29.5
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) 1.8 92 0.286 5.45 5.3 16278
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 1ZLQ 1.7 46.93 105673 5562 100 0.18909 0.18732 0.1869 0.22312 0.2235 RANDOM 23.615
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] -0.12 -0.53 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.771 r_dihedral_angle_4_deg 15.461 r_dihedral_angle_3_deg 12.974 r_dihedral_angle_1_deg 5.937 r_scangle_it 3.316 r_scbond_it 2.059 r_mcangle_it 1.64 r_angle_refined_deg 1.362 r_mcbond_it 1.303 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.771 r_dihedral_angle_4_deg 15.461 r_dihedral_angle_3_deg 12.974 r_dihedral_angle_1_deg 5.937 r_scangle_it 3.316 r_scbond_it 2.059 r_mcangle_it 1.64 r_angle_refined_deg 1.362 r_mcbond_it 1.303 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7890 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms 208
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling