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Crystal structure of CrmK, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 295 0.96 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.11 α = 94.73 b = 95.2 β = 96.56 c = 98.04 γ = 105.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2013-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.15 45.6 97 0.162 0.95 5 2.4 114678
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 2.15 2.27 96.1 0.699 0.7 2.4
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 5I1V 2.15 45.6 108921 5754 97.03 0.1707 0.1683 0.1762 0.2133 0.2185 RANDOM 34.51
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] 1.79 3 0.77 -1.3 0.32 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.686 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 15.907 r_dihedral_angle_1_deg 6.604 r_mcangle_it 3.597 r_mcbond_it 2.437 r_mcbond_other 2.436 r_angle_refined_deg 1.705 r_angle_other_deg 0.882 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.686 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 15.907 r_dihedral_angle_1_deg 6.604 r_mcangle_it 3.597 r_mcbond_it 2.437 r_mcbond_other 2.436 r_angle_refined_deg 1.705 r_angle_other_deg 0.882 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15536 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 272
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction