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Crystal Structure of hydroxymethylglutaryl-CoA lyase from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Tris 8.0, 3.4M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 4.41 72.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.012 α = 90 b = 189.012 β = 90 c = 189.012 γ = 90
Symmetry Space Group I 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH xenocs multilayer confocal mirror 2005-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-C 1.5418
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 2.4 80 99.6 0.086 0.086 12.7 42.6 22088 21999
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 2.4 2.44 100 0.53 0.53 9.97 42.6 1126
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 1YDN 2.4 80 22088 21999 735 99.6 0.18799 0.18799 0.18713 0.1882 0.21309 0.1746 RANDOM 36.229
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_3_deg 18.507 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_1_deg 8.317 r_scangle_it 3.581 r_scbond_it 2.139 r_angle_refined_deg 1.432 r_mcangle_it 1.202 r_mcbond_it 0.61 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_3_deg 18.507 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_1_deg 8.317 r_scangle_it 3.581 r_scbond_it 2.139 r_angle_refined_deg 1.432 r_mcangle_it 1.202 r_mcbond_it 0.61 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.126 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2238 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing ARP/wARP model building