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Crystal Structure of Homocysteine alpha-, gamma-lyase at 1.8 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E5F PDB ENTRY 1E5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 100 mM HEPES/NaOH (ph 7.5), 100 mM MgCl2, 15% w/v MPEG 2000, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 1.99 38.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.634 α = 90 b = 48.476 β = 110.33 c = 75.606 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
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 2.5 32.5 19864
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1E5F 2.5 32.5 1.86 19864 1035 97.8 0.1792 0.17975 0.17914 0.1788 0.20837 0.1999 RANDOM 20.266
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] -0.68 -0.96 0.64 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.341 r_scangle_it 2.882 r_scbond_it 1.68 r_angle_refined_deg 1.139 r_mcangle_it 1.079 r_mcbond_it 0.564 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.341 r_scangle_it 2.882 r_scbond_it 1.68 r_angle_refined_deg 1.139 r_mcangle_it 1.079 r_mcbond_it 0.564 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5040 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing