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Crystal structure of a flavin binding protein from Thermotoga Maritima, TM379
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 293 0.2M Na Citrate, 23% PEG 3350, 10% Glycerol, pH 7.5, EVAPORATION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.211 α = 90 b = 83.095 β = 116.93 c = 67.851 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 ADSC QUANTUM 4 2001-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97911 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 25 96.9 0.038 27 3.9 52473 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 82.2 0.299 4.1 2670
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 (All) 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 MAD 1.9 20 51065 5117 97.67 0.21859 0.21696 0.21696 0.2173 0.23347 0.2303 RANDOM 21.308
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] -0.7 0.34 0.91 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.372 r_scangle_it 2.524 r_dihedral_angle_1_deg 2.511 r_scbond_it 1.56 r_angle_refined_deg 1.126 r_mcangle_it 0.841 r_mcbond_it 0.448 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.372 r_scangle_it 2.524 r_dihedral_angle_1_deg 2.511 r_scbond_it 1.56 r_angle_refined_deg 1.126 r_mcangle_it 0.841 r_mcbond_it 0.448 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4346 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing