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The crystal structure of type II Dehydroquinase from Acidithiobacillus caldus SM-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15% PEG 8000, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.06 69.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.458 α = 90 b = 188.458 β = 90 c = 188.458 γ = 90
Symmetry Space Group F 41 3 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 PIXEL DECTRIS PILATUS3 S 6M 2016-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976270 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.95 94.23 91.1 0.066 0.068 0.016 1 22 16.8 19607
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 2.098 2.164 0.526 0.662 16.8
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 3LWZ 1.95 66.72 18564 1007 91.16 0.1644 0.1631 0.1735 0.1901 0.197 RANDOM 50.975
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 r_dihedral_angle_2_deg 28.761 r_dihedral_angle_3_deg 15.353 r_dihedral_angle_4_deg 15.073 r_dihedral_angle_1_deg 6.881 r_angle_refined_deg 1.691 r_angle_other_deg 1.469 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.761 r_dihedral_angle_3_deg 15.353 r_dihedral_angle_4_deg 15.073 r_dihedral_angle_1_deg 6.881 r_angle_refined_deg 1.691 r_angle_other_deg 1.469 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1115 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction