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Crystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound p-hydroxybenzaldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1USC PDB ENTRY 1USC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MORPHEUS SCREEN H5 10% W/V PEG 20 000, 20% V/V PEG MME 550; 0.02 M OF EACH AMINO ACID; 0.1 M MOPS/HEPES-NA PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.66 α = 90 b = 74.91 β = 90 c = 77.59 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 MARRESEARCH SX-165 2012-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 1.7 37.5 92.7 0.07 16 5.9 39042 3
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 1.7 1.8 96 0.48 3.3 6.2
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 1USC 1.85 37.46 24843 1308 79.59 0.24381 0.24196 0.2497 0.27771 0.282 RANDOM 19.267
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] 0.25 1.57 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.121 r_dihedral_angle_4_deg 18.605 r_dihedral_angle_3_deg 16.016 r_dihedral_angle_1_deg 7.013 r_angle_refined_deg 1.755 r_angle_other_deg 0.886 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.121 r_dihedral_angle_4_deg 18.605 r_dihedral_angle_3_deg 16.016 r_dihedral_angle_1_deg 7.013 r_angle_refined_deg 1.755 r_angle_other_deg 0.886 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 2756 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing