☰ Navigation Tabs
Crystal structure of fluoroacetate dehalogenase Daro3835 apoenzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 25% (W/V) PEG3350, 0.2 M MGCL2, 0.1 M BIS-TRIS PH 5.5, CRYOPROTECTANT 2% (V/V) PEG 200 AND PARATONE
Crystal Properties Matthews coefficient Solvent content 2 38.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.172 α = 87.625 b = 45.224 β = 75.565 c = 75.185 γ = 63.035
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 IV 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.86 19.66 94.3 0.049 0.044 0.997 17.7 3.6 40571 13.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.9 90.6 0.092 0.061 0.987 9.4 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1.86 19.66 2.07 40567 2127 94.35 0.1271 0.1246 0.1278 0.1735 0.1772 RANDOM 18.44
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.1949 f_angle_d 0.8973 f_chiral_restr 0.0555 f_bond_d 0.0077 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4642 Nucleic Acid Atoms Solvent Atoms 979 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PHENIX model building Coot model building