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Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii with bound p-hydroxybenzaldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R6V PDB ENTRY 2R6V
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 = 46.321 α = 90 b = 46.321 β = 90 c = 268.77 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 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 2.1 20 85.1 0.06 21.4 7.8 9300 4
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 2.1 2.2 90 0.25 4.3 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 2R6V 2.1 19.57 8389 442 81.46 0.24341 0.24202 0.26885 0.2517 RANDOM 25.634
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 0.89 0.89 -2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.712 r_dihedral_angle_4_deg 22.915 r_dihedral_angle_3_deg 18.156 r_dihedral_angle_1_deg 6.285 r_angle_refined_deg 1.719 r_chiral_restr 0.112 r_bond_refined_d 0.011 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 35.712 r_dihedral_angle_4_deg 22.915 r_dihedral_angle_3_deg 18.156 r_dihedral_angle_1_deg 6.285 r_angle_refined_deg 1.719 r_chiral_restr 0.112 r_bond_refined_d 0.011 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 1403 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing