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Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis (ligand free)
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 3.05 59.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.382 α = 90 b = 58.382 β = 90 c = 226.094 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 1.00 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 1.6 50.56 99.9 0.039 0.039 0.043 0.017 1 36.1 11.3 29697 3 17.4
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) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 100 0.229 0.229 0.251 0.1 9.5 11.6
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 (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 FREE R-VALUE 6KFA 1.6 50.56 29697 1573 99.85 0.15982 0.15845 0.1709 0.18575 0.1965 RANDOM 19.875
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] 0.5 0.25 0.5 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.579 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_4_deg 10.916 r_dihedral_angle_1_deg 6.752 r_long_range_B_refined 4.962 r_long_range_B_other 4.253 r_scangle_other 2.09 r_scbond_it 1.302 r_scbond_other 1.301 r_angle_refined_deg 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.579 r_dihedral_angle_3_deg 14.104 r_dihedral_angle_4_deg 10.916 r_dihedral_angle_1_deg 6.752 r_long_range_B_refined 4.962 r_long_range_B_other 4.253 r_scangle_other 2.09 r_scbond_it 1.302 r_scbond_other 1.301 r_angle_refined_deg 1.3 r_mcangle_it 1.205 r_mcangle_other 1.205 r_angle_other_deg 0.907 r_mcbond_it 0.729 r_mcbond_other 0.729 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 297 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing