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Crystal structure of a degv lipid binding protein (tm1468) from thermotoga maritima at 2.45 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 293 0.1M Cacodylate pH 6.5, 0.2M Mg(oAc)2, 27.5% PEG-8000, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 48.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.256 α = 90 b = 103.256 β = 90 c = 115.863 γ = 90
Symmetry Space Group P 41 21 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 APS sagitally focusing. 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2003-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 2.453 50 96.36 0.098 13.77 4.09 22755 43.04
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 2.453 2.55 97.78 0.293 4.88 3.89 2244
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 1mgp 2.45 47.16 21579 1174 96.28 0.18355 0.17987 0.187 0.25188 0.2535 RANDOM 24.207
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] 0.27 0.27 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.628 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 15.947 r_scangle_it 8.135 r_dihedral_angle_1_deg 6.044 r_scbond_it 5.82 r_mcangle_it 2.856 r_mcbond_it 2.262 r_angle_refined_deg 1.549 r_angle_other_deg 0.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.628 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 15.947 r_scangle_it 8.135 r_dihedral_angle_1_deg 6.044 r_scbond_it 5.82 r_mcangle_it 2.856 r_mcbond_it 2.262 r_angle_refined_deg 1.549 r_angle_other_deg 0.845 r_mcbond_other 0.584 r_nbd_refined 0.213 r_symmetry_vdw_other 0.193 r_nbd_other 0.19 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.139 r_chiral_restr 0.089 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4400 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 46
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement