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Crystal Structure of Human Riboflavin Kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 NA cadodalyte, Mg acetate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.096 α = 90 b = 57.096 β = 90 c = 82.505 γ = 120
Symmetry Space Group P 31 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 CUSTOM-MADE MIRROR 2002-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.0080 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.7 50 95.9 0.036 49.2 12.47 17010 -3 20.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 83.2 0.2 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.7 49.39 15843 861 94.36 0.186 0.184 0.1859 0.221 0.2255 RANDOM 15.5
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] -0.21 -0.11 -0.21 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.017 r_scangle_it 3.779 r_scbond_it 2.511 r_mcangle_it 1.907 r_angle_refined_deg 1.611 r_mcbond_it 1.042 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.017 r_scangle_it 3.779 r_scbond_it 2.511 r_mcangle_it 1.907 r_angle_refined_deg 1.611 r_mcbond_it 1.042 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1177 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling SOLVE phasing REFMAC refinement HKL-2000 data reduction