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The crystal structure of the iron free (Apo-)form of Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 277 8-10% Peg6000, 60mM Strontium Chloride, 0.1M ADA buffer, 15% Glycerol, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.55 65.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.033 α = 90 b = 188.033 β = 90 c = 82.047 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD CUSTOM-MADE 2001-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 3.2 20 92.4 0.065 12.2 53272 49227 -3 -3
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) 3.2 3.31 65.1 0.196
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1AFR 3.2 19.96 53272 47756 1471 92.51 0.22935 0.22935 0.2285 0.25709 0.2577 RANDOM 37.951
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] 3.75 1.88 3.75 -5.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.174 r_scangle_it 2.844 r_scbond_it 1.602 r_angle_refined_deg 1.516 r_mcangle_it 0.83 r_mcbond_it 0.372 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.174 r_scangle_it 2.844 r_scbond_it 1.602 r_angle_refined_deg 1.516 r_mcangle_it 0.83 r_mcbond_it 0.372 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16836 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing