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S-adenosyl homocysteine hydrolase (SAHH) from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GU1 PDB ENTRY 2Gu1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 3.03 59.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.35 α = 90 b = 136.05 β = 99.32 c = 191.87 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 100 CCD ADSC QUANTUM 315r mirrors 2009-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97930 ESRF ID23-1
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 1.9 45.55 181285
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Gu1 1.9 45.55 172196 9087 100 0.19815 0.19646 0.2306 0.2899 RANDOM 13.272
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] -0.11 0.02 -0.13 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.273 r_dihedral_angle_4_deg 17.213 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_1_deg 6.439 r_scangle_it 2.774 r_scbond_it 1.86 r_angle_refined_deg 1.508 r_mcangle_it 1.059 r_angle_other_deg 0.959 r_mcbond_it 0.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.273 r_dihedral_angle_4_deg 17.213 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_1_deg 6.439 r_scangle_it 2.774 r_scbond_it 1.86 r_angle_refined_deg 1.508 r_mcangle_it 1.059 r_angle_other_deg 0.959 r_mcbond_it 0.687 r_symmetry_vdw_other 0.27 r_nbd_refined 0.214 r_nbd_other 0.197 r_mcbond_other 0.195 r_symmetry_hbond_refined 0.177 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_other 0.131 r_chiral_restr 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 13392 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 235
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling