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Crystal structure of malonyl-CoA:Acyl carrier protein transacylase (MCAT) from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NM2 PDB ENTRY 1NM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 0.1M Hepes, 10% v/v PEG10000, 8% v/v MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.616 α = 90 b = 76.175 β = 101.22 c = 99.768 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV 2006-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 2.5 50 99.8 0.065 0.065 14.2 3.7 22318
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 2.5 2.59 100 0.452 0.452 2.8 3.6 2234
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 (All) 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 1NM2 2.5 36.7 22004 1126 98.29 0.217 0.215 0.2111 0.262 0.2629 RANDOM 55.749
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] 2.26 0.45 -0.73 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.988 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 20.301 r_dihedral_angle_1_deg 5.533 r_scangle_it 2.319 r_scbond_it 1.429 r_angle_refined_deg 1.409 r_mcangle_it 1.075 r_mcbond_it 0.607 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.988 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 20.301 r_dihedral_angle_1_deg 5.533 r_scangle_it 2.319 r_scbond_it 1.429 r_angle_refined_deg 1.409 r_mcangle_it 1.075 r_mcbond_it 0.607 r_nbtor_refined 0.304 r_nbd_refined 0.229 r_symmetry_hbond_refined 0.213 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4852 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction CNS phasing