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Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP(P 21 21 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 2.23 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.4 α = 90 b = 70.48 β = 90 c = 100.08 γ = 90
Symmetry Space Group P 21 21 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 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 1.65 35.24 95.7 0.05 18.5 5.3 36054 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 1.65 1.74 76.6 0.16 5.1 3
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 1.65 57.62 33438 2560 95.39 0.14577 0.14349 0.1571 0.17551 0.1862 RANDOM 17.154
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] 0.54 -0.39 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_3_deg 11.004 r_dihedral_angle_4_deg 7.494 r_dihedral_angle_1_deg 6.566 r_angle_refined_deg 1.772 r_mcangle_it 1.343 r_scbond_it 1.083 r_angle_other_deg 0.96 r_mcbond_it 0.785 r_mcbond_other 0.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.369 r_dihedral_angle_3_deg 11.004 r_dihedral_angle_4_deg 7.494 r_dihedral_angle_1_deg 6.566 r_angle_refined_deg 1.772 r_mcangle_it 1.343 r_scbond_it 1.083 r_angle_other_deg 0.96 r_mcbond_it 0.785 r_mcbond_other 0.782 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_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 2354 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing