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Crystal Structure of Native cis-CaaD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FLT PDB ENTRY 2FLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 9 298 three micro liter of 14 mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 8 M (NH4)2SO4, 0.1 M Bicine buffer (pH 9.0), hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.76 30.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.987 α = 90 b = 58.987 β = 90 c = 58.297 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 100 IMAGE PLATE RIGAKU RAXIS 2005-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.01 51.1 99.8 0.046 51.6 10.7 7768
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 2.01 2.08 99.2 0.09 9.8
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 2FLT 2.01 50 7398 356 99.88 0.18625 0.18384 0.1732 0.23574 0.2235 RANDOM 16.183
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] 0.26 0.13 0.26 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.17 r_dihedral_angle_3_deg 17.8 r_dihedral_angle_4_deg 17.688 r_rigid_bond_restr 5.925 r_dihedral_angle_1_deg 5.707 r_scbond_it 5.3 r_sphericity_free 4.866 r_scangle_it 4.508 r_sphericity_bonded 2.816 r_mcangle_it 1.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.17 r_dihedral_angle_3_deg 17.8 r_dihedral_angle_4_deg 17.688 r_rigid_bond_restr 5.925 r_dihedral_angle_1_deg 5.707 r_scbond_it 5.3 r_sphericity_free 4.866 r_scangle_it 4.508 r_sphericity_bonded 2.816 r_mcangle_it 1.605 r_angle_refined_deg 1.412 r_mcbond_it 0.968 r_symmetry_hbond_refined 0.392 r_nbtor_refined 0.307 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.224 r_symmetry_vdw_refined 0.185 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 912 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction CaspR phasing