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Crystal structure of IsdI in complex with heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZDP PDB ENTRY 2ZDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Bis-Tris buffer pH 5.5, and flash frozen with a cryoprotectant of 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.24 α = 90 b = 66.78 β = 90 c = 69.43 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 MARMOSAIC 300 mm CCD DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror. 2008-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-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 1.5 69.43 99.8 0.077 6.8 43991 43991
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 2ZDP 1.5 44.62 44056 43931 2217 99.71 0.213 0.183 0.181 0.1803 0.214 0.2113 RANDOM 21.709
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] -0.92 0.33 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.619 r_dihedral_angle_3_deg 11.337 r_dihedral_angle_4_deg 8.829 r_dihedral_angle_1_deg 5.879 r_scangle_it 2.97 r_scbond_it 1.939 r_mcangle_it 1.368 r_angle_refined_deg 1.118 r_rigid_bond_restr 0.935 r_mcbond_it 0.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.619 r_dihedral_angle_3_deg 11.337 r_dihedral_angle_4_deg 8.829 r_dihedral_angle_1_deg 5.879 r_scangle_it 2.97 r_scbond_it 1.939 r_mcangle_it 1.368 r_angle_refined_deg 1.118 r_rigid_bond_restr 0.935 r_mcbond_it 0.759 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1884 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 91
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction