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Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis, complexed with cyanide ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 5.0), 28-32% (w/v) PEG monomethyl ether 2000, 0.3 M NDSB-195
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.59 α = 90 b = 58.59 β = 90 c = 226.233 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 2M 2016-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 50.74 100 0.116 0.116 0.122 0.037 0.999 3 19.5 14405 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 100 0.598 0.598 0.627 0.187 0.971 5.3 20.5
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 (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 6KFA 2.1 50.74 13571 751 99.92 0.18961 0.18733 0.1968 0.23171 0.2456 RANDOM 32.195
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] 1.01 0.5 1.01 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.551 r_dihedral_angle_3_deg 13.464 r_dihedral_angle_4_deg 9.697 r_dihedral_angle_1_deg 6.908 r_long_range_B_refined 6.668 r_long_range_B_other 6.469 r_scangle_other 5.299 r_scbond_it 3.395 r_scbond_other 3.356 r_mcangle_it 2.632
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.551 r_dihedral_angle_3_deg 13.464 r_dihedral_angle_4_deg 9.697 r_dihedral_angle_1_deg 6.908 r_long_range_B_refined 6.668 r_long_range_B_other 6.469 r_scangle_other 5.299 r_scbond_it 3.395 r_scbond_other 3.356 r_mcangle_it 2.632 r_mcangle_other 2.631 r_mcbond_it 1.917 r_mcbond_other 1.917 r_angle_refined_deg 1.66 r_angle_other_deg 0.989 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1280 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing