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Crystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound 1-Cyclohex-2-enone
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 12.5% PEG 1000, 12.5% W/V PEG 3350, 12.5% V/V MPD AND 0.1 M ACETATE BUFFER PH 4.5
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.771 α = 90 b = 73.791 β = 90.07 c = 77.374 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 225 mm CCD 2011-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.65 30 99.4 0.05 16.5 4.2 86300 2.3
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 1.65 1.75 97 0.64 2.3 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1USC 1.65 29.53 81653 4235 99.16 0.16236 0.16111 0.18599 0.1897 RANDOM 23.136
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] 4.04 1.51 15.28 -19.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.577 r_dihedral_angle_4_deg 15.453 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 6.251 r_angle_refined_deg 1.242 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.577 r_dihedral_angle_4_deg 15.453 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 6.251 r_angle_refined_deg 1.242 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 5602 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing