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Crystal Structure of Human Lyase R41M in complex with HMG-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MP4 PDB entry 3MP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 PEG8K, Hepes buffer, MgCl2 and HMG-CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.44 49.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.98 α = 90 b = 116.66 β = 112.16 c = 86.52 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 315 2007-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 28.35 100 0.101 15.9 5 86171 -3 30.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.33 99.9 0.674 2.1 4.6 8582
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 3MP4 2.25 28.35 81864 8220 94.8 0.221 0.221 0.2205 0.271 0.2706 RANDOM 37.3
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] 1.91 8.99 0.6 -2.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 2.57 c_mcangle_it 2 c_scbond_it 1.78 c_angle_deg 1.2 c_mcbond_it 1.2 c_improper_angle_d 0.83 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 2.57 c_mcangle_it 2 c_scbond_it 1.78 c_angle_deg 1.2 c_mcbond_it 1.2 c_improper_angle_d 0.83 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13034 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 60
Software Software Software Name Purpose ADSC data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing