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CRYSTAL STRUCTURE OF RIBOFLAVIN KINASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NB0 PDB ENTRY 1NB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 NA CACODALYTE, MG ACETATE, PEG 8000 , pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.097 α = 90 b = 57.097 β = 90 c = 82.482 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 IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRROR 2002-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.8 30 99.3 0.053 21.4 4 14856 -3 28.35
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 1.8 1.86 95.2 0.854 1.2 3.4
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 1NB0 1.8 28.55 13300 719 94 0.188 0.186 0.1886 0.227 0.2295 RANDOM 22.07
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] 0.66 0.33 0.66 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.754 r_scangle_it 4.066 r_scbond_it 2.552 r_mcangle_it 1.823 r_angle_refined_deg 1.666 r_mcbond_it 1.017 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.754 r_scangle_it 4.066 r_scbond_it 2.552 r_mcangle_it 1.823 r_angle_refined_deg 1.666 r_mcbond_it 1.017 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.114 r_bond_refined_d 0.017 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 108 Heterogen Atoms 59
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction