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Crystal structure of riboflavin kinase from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Hybrid model generated by Rosetta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 290 20% PEG 3350, 0.28M KF, 0.1M HEPES, 5mM DTT, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.92 36.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.695 α = 90 b = 65.604 β = 103.49 c = 62.69 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 325 mm CCD 2005-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97915 SSRL BL9-2
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 2.4 38.6 88 0.064 10.9 3.3 10719 10719 52
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 Hybrid model generated by Rosetta 2.4 20 10179 510 86.73 0.21616 0.2128 0.2153 0.28857 0.281 RANDOM 25.677
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] -0.47 0.01 1.11 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.07 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_4_deg 13.42 r_dihedral_angle_1_deg 5.622 r_scangle_it 1.017 r_angle_refined_deg 0.961 r_angle_other_deg 0.765 r_mcangle_it 0.719 r_scbond_it 0.713 r_mcbond_it 0.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.07 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_4_deg 13.42 r_dihedral_angle_1_deg 5.622 r_scangle_it 1.017 r_angle_refined_deg 0.961 r_angle_other_deg 0.765 r_mcangle_it 0.719 r_scbond_it 0.713 r_mcbond_it 0.422 r_nbtor_refined 0.181 r_nbd_refined 0.172 r_nbd_other 0.172 r_symmetry_vdw_other 0.166 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.136 r_symmetry_vdw_refined 0.107 r_nbtor_other 0.082 r_mcbond_other 0.056 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2494 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling SOLVE phasing