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Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis bound with thiocyanate
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, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.095 α = 90 b = 58.095 β = 90 c = 225.955 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 1.1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.55 49.11 99.9 0.049 0.049 34.7 18.7 34043 3 19.4
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 1.55 1.63 99.6 0.525 0.552 0.552 0.133 0.974 16.9 16.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6KFA 1.55 49.11 32225 1722 99.8 0.171 0.17 0.191 0.193 RANDOM 19.12
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] 0.36 0.18 0.36 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.884 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_4_deg 12.128 r_dihedral_angle_1_deg 6.429 r_long_range_B_refined 4.542 r_long_range_B_other 4.126 r_scangle_other 1.987 r_angle_refined_deg 1.297 r_scbond_it 1.26 r_scbond_other 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.884 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_4_deg 12.128 r_dihedral_angle_1_deg 6.429 r_long_range_B_refined 4.542 r_long_range_B_other 4.126 r_scangle_other 1.987 r_angle_refined_deg 1.297 r_scbond_it 1.26 r_scbond_other 1.26 r_mcangle_it 1.183 r_mcangle_other 1.182 r_angle_other_deg 0.906 r_mcbond_it 0.728 r_mcbond_other 0.728 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 227 Heterogen Atoms 27
Software Software Software Name Purpose XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement