☰ Navigation Tabs
Crystal structure of holo-H44A mutant of Hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1, in complex with Hydroxypyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277.15 HEPES, Sodium Citrate
Crystal Properties Matthews coefficient Solvent content 1.91 35.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.914 α = 90 b = 70.914 β = 90 c = 222.572 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 PIXEL DECTRIS EIGER X 16M 2019-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9766 PETRA III, EMBL c/o DESY P14 (MX2)
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 53.77 96.3 0.083 0.116 0.081 0.998 7.3 2.6 29321
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 0.835 1.154 0.794 0.378 2.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6R62 1.95 53.769 29316 1484 96.273 0.164 0.1618 0.1622 0.212 0.2126 32.704
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] 5.32 5.32 -10.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.652 r_dihedral_angle_4_deg 17.226 r_dihedral_angle_3_deg 14.189 r_dihedral_angle_1_deg 7.251 r_lrange_it 5.475 r_lrange_other 5.46 r_scangle_it 4.129 r_scangle_other 4.129 r_mcangle_it 3.737 r_mcangle_other 3.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.652 r_dihedral_angle_4_deg 17.226 r_dihedral_angle_3_deg 14.189 r_dihedral_angle_1_deg 7.251 r_lrange_it 5.475 r_lrange_other 5.46 r_scangle_it 4.129 r_scangle_other 4.129 r_mcangle_it 3.737 r_mcangle_other 3.736 r_scbond_it 3.309 r_scbond_other 3.3 r_mcbond_other 3.144 r_mcbond_it 3.143 r_angle_refined_deg 1.633 r_angle_other_deg 1.327 r_xyhbond_nbd_refined 0.212 r_nbd_other 0.212 r_nbd_refined 0.208 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.178 r_metal_ion_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.123 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.08 r_xyhbond_nbd_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3727 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing