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human formylglycine generating enzyme, C336S mutant, iodide co-crystallization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 4000, Calcium iodide, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.89 α = 90 b = 109.11 β = 90 c = 43.492 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2006-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5419
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 1.99 50 96.8 0.132 9 3.6 72271
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 1.99 2.06 0.413 1.9 2.3 1570
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 2aij 2 33.83 19211 963 97.93 0.17492 0.17183 0.1847 0.23785 0.2494 RANDOM 25.822
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] 0.06 0.97 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.179 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_3_deg 13.445 r_dihedral_angle_1_deg 6.719 r_scangle_it 2.535 r_scbond_it 1.604 r_angle_refined_deg 1.264 r_mcangle_it 1.195 r_angle_other_deg 0.873 r_mcbond_it 0.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.179 r_dihedral_angle_4_deg 16.002 r_dihedral_angle_3_deg 13.445 r_dihedral_angle_1_deg 6.719 r_scangle_it 2.535 r_scbond_it 1.604 r_angle_refined_deg 1.264 r_mcangle_it 1.195 r_angle_other_deg 0.873 r_mcbond_it 0.694 r_nbd_other 0.21 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.163 r_mcbond_other 0.144 r_symmetry_vdw_other 0.141 r_symmetry_vdw_refined 0.139 r_metal_ion_refined 0.1 r_nbtor_other 0.093 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2176 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling