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Crystal structure of IsdI in complex with Cobalt protoporphyrin IX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XBW PDB ENTRY 1XBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.32 α = 90 b = 65.668 β = 107.81 c = 58.66 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315 2007-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1 SSRL BL7-1
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 56 0.045 10.9 3.5 39272 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.54 0.323
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 1XBW 1.5 55.81 39272 2079 95.74 0.18233 0.18135 0.1784 0.2011 0.1976 RANDOM 15.929
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 0.37 0.32 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.797 r_dihedral_angle_3_deg 10.45 r_dihedral_angle_4_deg 9.732 r_dihedral_angle_1_deg 5.918 r_scangle_it 2.983 r_scbond_it 1.962 r_mcangle_it 1.417 r_angle_refined_deg 1.258 r_mcbond_it 0.93 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.797 r_dihedral_angle_3_deg 10.45 r_dihedral_angle_4_deg 9.732 r_dihedral_angle_1_deg 5.918 r_scangle_it 2.983 r_scbond_it 1.962 r_mcangle_it 1.417 r_angle_refined_deg 1.258 r_mcbond_it 0.93 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1832 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing