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Crystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound benzene-1,4-diol
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 D8 12.5% W/V PEG 1000, 12.5% W/V PEG 3350, 12.5% V/V MPD; 0.02 M OF EACH ALCOHOL; 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 = 64.524 α = 90 b = 74.618 β = 90 c = 77.743 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 2012-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.15 50 99 0.1 12.7 9.3 20947 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 2.15 2.28 96.8 0.59 3.4 8.3
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 1USC 2.15 48.85 19869 1074 98.96 0.19455 0.19165 0.198 0.2495 0.255 RANDOM 48.93
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] 0.89 4.49 -5.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_4_deg 22.609 r_dihedral_angle_3_deg 16.507 r_dihedral_angle_1_deg 6.189 r_angle_refined_deg 1.526 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_4_deg 22.609 r_dihedral_angle_3_deg 16.507 r_dihedral_angle_1_deg 6.189 r_angle_refined_deg 1.526 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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 2804 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing