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Crystal structure of acyl-carrier-protein-S-malonyltransferase from Bartonella henselae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 BaheA.00141.a.A1 PS00852 at 21.8 mg/mL against JCSG+ screen condition A5, 0.2 M magnesium formate, 20% PEG 3350 with 25% EG as cryo-protectant, crystal tracking ID 218778a5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.19 α = 90 b = 98.01 β = 90 c = 138.18 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2010-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
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 1.6 50 98.8 0.07 20.24 8.1 90747 89635 -3 21.638
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) 1.6 1.64 87.4 0.46 3.5 5.2 6624
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 (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 3ezo 1.6 50 90747 89375 4475 98.5 0.1597 0.1585 0.1626 0.1823 0.1864 RANDOM 15.6705
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] -0.01 -0.47 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.556 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_3_deg 11.857 r_dihedral_angle_1_deg 5.406 r_scangle_it 3.642 r_scbond_it 2.167 r_angle_refined_deg 1.374 r_mcangle_it 1.264 r_mcbond_it 0.715 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.556 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_3_deg 11.857 r_dihedral_angle_1_deg 5.406 r_scangle_it 3.642 r_scbond_it 2.167 r_angle_refined_deg 1.374 r_mcangle_it 1.264 r_mcbond_it 0.715 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4546 Nucleic Acid Atoms Solvent Atoms 811 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction