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Unravelling structure of riboflavin synthase for designing of potential anti-bacterial drug
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 288.15 0.2 M Ammonium Sulfate,
0.1M MES monohydrate (pH 6.5),
10% w/v PEG MME 5000
Crystal Properties Matthews coefficient Solvent content 2.94 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.559 α = 90 b = 130.632 β = 90 c = 202.5 γ = 90
Symmetry Space Group C 2 2 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 PIXEL RIGAKU dextris 200k 2019-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 3.19 40 97.4 0.163 9.2 4.4 13224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 99.9 0.464 0.818 2.9 4.6
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 1I8D 3.19 27.26 12554 636 97.23 0.2204 0.2182 0.2197 0.2638 0.2595 RANDOM 39.875
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] 0.31 -2.54 2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.415 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_3_deg 18.418 r_dihedral_angle_1_deg 8.193 r_angle_refined_deg 1.615 r_angle_other_deg 1.251 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.415 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_3_deg 18.418 r_dihedral_angle_1_deg 8.193 r_angle_refined_deg 1.615 r_angle_other_deg 1.251 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4604 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 14
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction