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Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP (P3 2 21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X0K PDB ENTRY 2X0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 26-30% PEG 4000, 200 MM LI2SO4 AND 100 MM SODIUM ACETATE PH 5.0 AND 100 MM NAI
Crystal Properties Matthews coefficient Solvent content 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.59 α = 90 b = 73.59 β = 90 c = 149.69 γ = 120
Symmetry Space Group P 32 2 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.8 36.79 98 0.06 15.8 4.5 43268 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 1.8 1.9 89.6 0.2 4 3.8
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 2X0K 1.8 63.81 40167 3101 97.64 0.17471 0.17256 0.1727 0.2027 0.2027 RANDOM 20.913
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] 0.03 0.02 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.892 r_dihedral_angle_3_deg 11.956 r_dihedral_angle_4_deg 8.891 r_dihedral_angle_1_deg 6.369 r_angle_refined_deg 1.477 r_mcangle_it 1.467 r_scbond_it 1.062 r_mcbond_it 0.842 r_chiral_restr 0.107 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.892 r_dihedral_angle_3_deg 11.956 r_dihedral_angle_4_deg 8.891 r_dihedral_angle_1_deg 6.369 r_angle_refined_deg 1.477 r_mcangle_it 1.467 r_scbond_it 1.062 r_mcbond_it 0.842 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2378 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing