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Crystal structure of acyl-carrier-protein s-malonyltransferase from burkholderia pseudomallei 1710b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MLA 1mla modified with ccp4 chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 JCSG+ SCREEN H3: 100MM BISTRIS PH 5.5, 25% PEG 3350, VAPOR DIFFUSION, TEMPERATURE 290K, pH 5.50, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.92 α = 90 b = 117.47 β = 90 c = 44.53 γ = 90
Symmetry Space Group P 21 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 RIGAKU SATURN 944 2008-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.05 50 96.4 0.083 19.24 6.9 18128 18128 -3 20.89
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 2.05 2.1 76.4 0.24 7.6 5.4 1030
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 MR, MR THROUGHOUT 1mla modified with ccp4 chainsaw 2.05 40.13 18098 18098 914 96.5 0.158 0.158 0.155 0.1576 0.208 0.2087 RANDOM 12.75
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] -1.23 -1.57 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.68 r_dihedral_angle_4_deg 13.46 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 5.545 r_scangle_it 4.232 r_scbond_it 2.573 r_angle_refined_deg 1.488 r_mcangle_it 1.452 r_angle_other_deg 0.98 r_mcbond_it 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.68 r_dihedral_angle_4_deg 13.46 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 5.545 r_scangle_it 4.232 r_scbond_it 2.573 r_angle_refined_deg 1.488 r_mcangle_it 1.452 r_angle_other_deg 0.98 r_mcbond_it 0.798 r_mcbond_other 0.212 r_chiral_restr 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2210 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling