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Crystal structure of IsdI-W66Y in complex with heme and cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LGN PDB ENTRY 3LGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 Crystals were grown in a reservoir solution containing 25% w/v polyethylene glycol 3350, 0.2 M magnesium chloride, and 0.1 M Bis-Tris, pH 5.5, and flash frozen with a cryoprotectant of 20% ethylene glycol and 20 mM sodium cyanide solution., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.311 α = 90 b = 67.014 β = 90 c = 69.567 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 100 CCD RIGAKU SATURN 944+ Varimax-VHF optics 2011-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 1.8 50 99.9 0.095 15.475 9.9 25378 25378
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 3LGN 1.8 25.267 24090 24090 1288 96.4 0.19937 0.19937 0.19727 0.1963 0.23842 0.2375 RANDOM 18.886
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] -0.08 0.06 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.905 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_4_deg 11.165 r_dihedral_angle_1_deg 5.962 r_scangle_it 2.813 r_scbond_it 1.753 r_mcangle_it 1.258 r_angle_refined_deg 1.187 r_mcbond_it 0.667 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.905 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_4_deg 11.165 r_dihedral_angle_1_deg 5.962 r_scangle_it 2.813 r_scbond_it 1.753 r_mcangle_it 1.258 r_angle_refined_deg 1.187 r_mcbond_it 0.667 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1830 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling