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Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis (recombinant)
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 = 57.924 α = 90 b = 57.924 β = 90 c = 226.321 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 CCD ADSC QUANTUM 315r 2016-03-18 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) 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 50.16 99.99 19.6 14.8 15329
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 2.11 100 0.72 0.765 0.765 0.192 0.95 4.7 15.2
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 50.16 15329 821 99.99 0.1598 0.15747 0.1687 0.20513 0.2158 RANDOM 23.497
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] 0.76 0.38 0.76 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.496 r_dihedral_angle_3_deg 13.591 r_dihedral_angle_4_deg 9.705 r_dihedral_angle_1_deg 6.744 r_long_range_B_refined 5.036 r_long_range_B_other 4.833 r_scangle_other 3.356 r_scbond_it 2.031 r_scbond_other 2.03 r_mcangle_it 1.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.496 r_dihedral_angle_3_deg 13.591 r_dihedral_angle_4_deg 9.705 r_dihedral_angle_1_deg 6.744 r_long_range_B_refined 5.036 r_long_range_B_other 4.833 r_scangle_other 3.356 r_scbond_it 2.031 r_scbond_other 2.03 r_mcangle_it 1.743 r_mcangle_other 1.743 r_angle_refined_deg 1.435 r_mcbond_it 1.238 r_mcbond_other 1.175 r_angle_other_deg 0.969 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 170 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing