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Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii 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 VAPOR DIFFUSION 293 VAPOR DIFFUSION AT 293K; CONDITIONS CONTAINING PEG 3350 OR 6000 (10-20% W/V) AS PRECIPITATION AGENT AND DIFFERENT SALTS (50-200 MM MAGNESIUM CLORIDE, POTASSIUM FORMATE, NATRIUM FORMATE, AMMONIUM FORMATE, MAGNESIUM FORMATE)
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.06 α = 90 b = 46.06 β = 90 c = 268.6 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2011-02-12 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 1.75 45 100 0.06 26.2 15.3 18259 3.5
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 1.75 1.85 100 0.64 3.5 10.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1USC 1.75 44.77 17346 913 99.98 0.19629 0.19445 0.194 0.23149 0.2292 RANDOM 30.728
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] 0.61 0.61 0.61 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.626 r_dihedral_angle_4_deg 20.153 r_dihedral_angle_3_deg 15.131 r_dihedral_angle_1_deg 5.724 r_angle_refined_deg 1.287 r_chiral_restr 0.096 r_bond_refined_d 0.008 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 35.626 r_dihedral_angle_4_deg 20.153 r_dihedral_angle_3_deg 15.131 r_dihedral_angle_1_deg 5.724 r_angle_refined_deg 1.287 r_chiral_restr 0.096 r_bond_refined_d 0.008 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 1437 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing