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Crystal Structure of aq_1716 from Aquifex Aeolicus VF5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C07 PDB ENTRY 2C07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 USING 4 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.8 mg/ml) AND RESERVOIR SOLUTION CONTAINING 45% v/v PEG200, 0.1M Tris-HCl (pH 6.4), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.698 α = 90 b = 64.214 β = 90 c = 73.448 γ = 90
Symmetry Space Group P 21 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 MARMOSAIC 300 mm CCD ROSENBAUM 2006-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97243 APS 22-ID
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 1.84 50 99.7 0.089 20.3 23.7 43626 43626
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 1.84 1.92 98.2 0.266 11.1 4198
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 PDB ENTRY 2C07 1.84 30 43574 2186 99.36 0.185 0.183 0.1829 0.223 0.2218 RANDOM 19.301
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] -1.51 0.58 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 21.093 r_dihedral_angle_3_deg 12.582 r_dihedral_angle_1_deg 5.473 r_scangle_it 3.086 r_scbond_it 1.898 r_angle_refined_deg 1.091 r_mcangle_it 1.033 r_mcbond_it 0.65 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 21.093 r_dihedral_angle_3_deg 12.582 r_dihedral_angle_1_deg 5.473 r_scangle_it 3.086 r_scbond_it 1.898 r_angle_refined_deg 1.091 r_mcangle_it 1.033 r_mcbond_it 0.65 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.224 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3683 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction AMoRE phasing