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Crystal structure of human 3-hydroxy-3-methylglutaryl CoA synthase I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FA0 PDB entries 2FA0,2F82,2FA3,2F9A,1XPL experimental model PDB 2F82 PDB entries 2FA0,2F82,2FA3,2F9A,1XPL experimental model PDB 2FA3 PDB entries 2FA0,2F82,2FA3,2F9A,1XPL experimental model PDB 2F9A PDB entries 2FA0,2F82,2FA3,2F9A,1XPL experimental model PDB 1XPL PDB entries 2FA0,2F82,2FA3,2F9A,1XPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 297 0.2M (NH4)2SO4, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.762 α = 90 b = 92.762 β = 90 c = 235.532 γ = 90
Symmetry Space Group P 43 21 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 CCD MARMOSAIC 225 mm CCD 2006-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 94.4 0.128 5 66668 66668
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.7 0.722 6.1
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 entries 2FA0,2F82,2FA3,2F9A,1XPL 2 50 63108 63108 3380 94.5 0.16149 0.16149 0.15933 0.171 0.20227 0.2104 RANDOM 24.337
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] 0.22 0.22 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.212 r_dihedral_angle_4_deg 17.088 r_dihedral_angle_3_deg 12.14 r_scangle_it 7.182 r_dihedral_angle_1_deg 6.02 r_scbond_it 5.87 r_mcangle_it 3.463 r_mcbond_it 2.52 r_angle_other_deg 1.378 r_angle_refined_deg 1.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.212 r_dihedral_angle_4_deg 17.088 r_dihedral_angle_3_deg 12.14 r_scangle_it 7.182 r_dihedral_angle_1_deg 6.02 r_scbond_it 5.87 r_mcangle_it 3.463 r_mcbond_it 2.52 r_angle_other_deg 1.378 r_angle_refined_deg 1.345 r_mcbond_other 0.654 r_symmetry_vdw_other 0.227 r_nbd_refined 0.205 r_nbd_other 0.192 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.142 r_nbtor_other 0.093 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7135 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing