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X-ray structure of the diatomic oxo-intermediate NikA/1-Int', prior hydroxylation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZLQ PDB ID 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 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.985 α = 90 b = 95.172 β = 90 c = 125.049 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 Mirrors 2009-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9796 ESRF BM30A
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 2.5 43.5 94 0.106 7.86 2.3 34625 36.9
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) 2.5 88 0.313 3.3 2.4 6716
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 ID 1ZLQ 2.5 43.49 34625 1823 100 0.17645 0.17262 0.1768 0.249 0.2493 RANDOM 21.989
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] -0.24 -0.16 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.587 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 17.486 r_dihedral_angle_1_deg 6.809 r_scangle_it 3.493 r_scbond_it 2.132 r_angle_refined_deg 1.716 r_mcangle_it 1.276 r_mcbond_it 0.669 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.587 r_dihedral_angle_4_deg 19.562 r_dihedral_angle_3_deg 17.486 r_dihedral_angle_1_deg 6.809 r_scangle_it 3.493 r_scbond_it 2.132 r_angle_refined_deg 1.716 r_mcangle_it 1.276 r_mcbond_it 0.669 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7864 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement