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Crystal structure of human cystathionase (Cystathionine gamma lyase) in complex with DL-propargylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMP PDB entry 2NMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 293 0.2M Di-ammonium hydrogen citrate, 20% PEG 3350. Streak seeding used, apo crystal soaked with inhibitor, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.35 α = 90 b = 107.22 β = 90 c = 153.31 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD Double mirrors 2006-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 2 20 92.9 0.123 0.123 13.81 6.7 109200 109200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 98.9 0.469 0.445 3.2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 2NMP 2 19.91 103738 103738 5460 100 0.16061 0.15831 0.164 0.20406 0.2061 RANDOM 14.036
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] -0.79 -0.11 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.618 r_dihedral_angle_4_deg 19.156 r_dihedral_angle_3_deg 15.029 r_dihedral_angle_1_deg 6.201 r_scangle_it 2.896 r_scbond_it 1.999 r_angle_refined_deg 1.374 r_mcangle_it 1.189 r_angle_other_deg 0.931 r_mcbond_it 0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.618 r_dihedral_angle_4_deg 19.156 r_dihedral_angle_3_deg 15.029 r_dihedral_angle_1_deg 6.201 r_scangle_it 2.896 r_scbond_it 1.999 r_angle_refined_deg 1.374 r_mcangle_it 1.189 r_angle_other_deg 0.931 r_mcbond_it 0.808 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.201 r_nbd_other 0.196 r_mcbond_other 0.177 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_other 0.146 r_chiral_restr 0.119 r_symmetry_vdw_refined 0.107 r_nbtor_other 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11836 Nucleic Acid Atoms Solvent Atoms 1160 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing