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Human selenocysteine lyase, P1 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GZC PDB ENTRY 3GZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 293 50mM HEPES, 200mM Ammonium Nitrate, 25% PEG 3350, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.64 α = 83.91 b = 72.2 β = 68.39 c = 89.43 γ = 86.96
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 mirrors 2006-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9800 ESRF BM14
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 1.8 30 94.1 0.051 0.123 16.2 2 134466 134466
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 1.8 1.9 93.5 0.527 0.743 2.2 2 20018
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 (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 3GZC 1.8 29.59 127741 127741 6724 100 0.1854 0.1854 0.18373 0.1976 0.21731 0.2305 RANDOM 12.632
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] 0.24 0.05 0.59 0.49 0.03 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.651 r_dihedral_angle_4_deg 17.987 r_dihedral_angle_3_deg 15.515 r_dihedral_angle_1_deg 5.601 r_scangle_it 3.062 r_angle_other_deg 2.8 r_scbond_it 2.013 r_angle_refined_deg 1.455 r_mcangle_it 1.211 r_mcbond_it 0.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.651 r_dihedral_angle_4_deg 17.987 r_dihedral_angle_3_deg 15.515 r_dihedral_angle_1_deg 5.601 r_scangle_it 3.062 r_angle_other_deg 2.8 r_scbond_it 2.013 r_angle_refined_deg 1.455 r_mcangle_it 1.211 r_mcbond_it 0.703 r_mcbond_other 0.185 r_chiral_restr 0.122 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12162 Nucleic Acid Atoms Solvent Atoms 898 Heterogen Atoms 76
Software Software Software Name Purpose ProDC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling