☰ Navigation Tabs
Crystal structure of holo-F210W mutant of Hydroxy ketone aldolase (SwHKA)from Sphingomonas wittichii RW1
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 35.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.996 α = 90 b = 70.996 β = 90 c = 222.817 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 PILATUS 6M-F 2019-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97620 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.2 74.27 100 0.078 0.087 0.039 0.999 15.5 9.7 130983
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 1.2 1.22 0.478 0.539 0.247 0.906 9.5
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 1.2 53.889 130980 6604 99.987 0.12 0.1185 0.1183 0.1463 0.1461 11.71
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] -0.091 -0.046 -0.091 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.328 r_dihedral_angle_4_deg 17.052 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 5.915 r_rigid_bond_restr 4.075 r_lrange_it 2.493 r_scangle_it 2.398 r_scangle_other 2.398 r_scbond_it 2.152 r_scbond_other 2.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.328 r_dihedral_angle_4_deg 17.052 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 5.915 r_rigid_bond_restr 4.075 r_lrange_it 2.493 r_scangle_it 2.398 r_scangle_other 2.398 r_scbond_it 2.152 r_scbond_other 2.132 r_lrange_other 2.12 r_angle_refined_deg 2.019 r_angle_other_deg 1.669 r_mcangle_other 1.321 r_mcangle_it 1.32 r_mcbond_it 1.122 r_mcbond_other 1.12 r_symmetry_xyhbond_nbd_other 0.473 r_symmetry_nbd_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.265 r_nbd_other 0.262 r_xyhbond_nbd_refined 0.234 r_nbd_refined 0.227 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.179 r_chiral_restr 0.127 r_ncsr_local_group_1 0.091 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3753 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing