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Xray structure of Blc dimer in complex with vaccenic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QWD PDB entry 1QWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 sodium citrate 800-900 mM, sodium borate 50 mM, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.901 α = 90 b = 81.337 β = 90 c = 89.02 γ = 90
Symmetry Space Group P 21 21 21
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 2004-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0332 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 59.76 99.75 0.089 0.137 37259 37259
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) 1.8 1.85 89.1 0.327 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1QWD 1.8 59.76 37259 37259 2314 99.75 0.17325 0.17325 0.17093 0.184 0.21027 0.2188 RANDOM 15.212
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] 0.6 -0.52 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.864 r_scangle_it 3.689 r_scbond_it 2.221 r_mcangle_it 1.3 r_angle_refined_deg 1.289 r_angle_other_deg 0.793 r_mcbond_it 0.679 r_symmetry_vdw_other 0.294 r_nbd_other 0.258 r_nbd_refined 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.864 r_scangle_it 3.689 r_scbond_it 2.221 r_mcangle_it 1.3 r_angle_refined_deg 1.289 r_angle_other_deg 0.793 r_mcbond_it 0.679 r_symmetry_vdw_other 0.294 r_nbd_other 0.258 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.207 r_symmetry_hbond_refined 0.205 r_symmetry_vdw_refined 0.157 r_chiral_restr 0.086 r_nbtor_other 0.082 r_bond_refined_d 0.011 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2684 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing