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Crystal structure of human Cystathionine gamma lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8P PDB ENTRY 1N8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 15% PEG3350, 200mM Ammonium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.78 α = 90 b = 107.57 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 ADSC QUANTUM 315 liquid nitrogen cooled channel-cut silicon monochromator, a cylindrical grazing incidence mirror 2006-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.03320 ESRF ID29
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 2.6 30 99.8 0.14 0.225 7.2 7.3 54383 54383
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 2.6 2.7 99.3 0.338 0.517 3.4 7.3 5730
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1N8P 2.6 19.93 2 2 51628 51628 2718 100 0.18035 0.18035 0.17694 0.1725 0.24454 0.2378 RANDOM 24.756
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] -2.51 -0.17 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.413 r_dihedral_angle_4_deg 23.786 r_dihedral_angle_3_deg 20.571 r_dihedral_angle_1_deg 7.364 r_scangle_it 2.977 r_scbond_it 1.879 r_angle_refined_deg 1.64 r_mcangle_it 1.126 r_mcbond_it 0.648 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.413 r_dihedral_angle_4_deg 23.786 r_dihedral_angle_3_deg 20.571 r_dihedral_angle_1_deg 7.364 r_scangle_it 2.977 r_scbond_it 1.879 r_angle_refined_deg 1.64 r_mcangle_it 1.126 r_mcbond_it 0.648 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.109 r_symmetry_hbond_refined 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11846 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling MOLREP phasing