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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 2Y08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 295 0.96 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.63 α = 95.18 b = 95.73 β = 96.98 c = 98.44 γ = 104.39
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 300 mm plate 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 1.84 96.94 95.9 0.118 0.993 7.5 4 184445 22.5
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 1.84 1.94 94.7 0.828 0.8 3.9
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 2Y08 1.84 96.94 175148 9296 95.93 0.1625 0.1608 0.1691 0.1936 0.1986 RANDOM 30.26
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] 1.22 1.45 0.21 -0.29 0.02 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.743 r_dihedral_angle_4_deg 20.465 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_1_deg 6.271 r_mcangle_it 2.763 r_mcbond_it 1.918 r_mcbond_other 1.913 r_angle_refined_deg 1.673 r_angle_other_deg 0.894 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.743 r_dihedral_angle_4_deg 20.465 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_1_deg 6.271 r_mcangle_it 2.763 r_mcbond_it 1.918 r_mcbond_other 1.913 r_angle_refined_deg 1.673 r_angle_other_deg 0.894 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15553 Nucleic Acid Atoms Solvent Atoms 1386 Heterogen Atoms 212
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction