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Structure of the Acyl Transferase domain of ZmaA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 mother liquor 200 mM MgCl2, 20% PEG 4000, 800 mM sodium formate, 100 mM BisTris; drops equal volume 7 mg/ml protein and mother liquor, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.915 α = 90 b = 74.25 β = 90 c = 124.728 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 IMAGE PLATE MAR scanner 300 mm plate 2009-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97872 APS 21-ID-D
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 1.65 25 99.9 0.049 27.7 6.9 54447 54382 20.8
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) 1 1.65 1.68 100 0.363 4.1 6 2669
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 SAD + molecular replacement THROUGHOUT 2QO3 1.7 24.51 46364 46276 2478 99.81 0.17257 0.17257 0.17108 0.171 0.20046 0.2005 RANDOM 22.131
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] -0.1 0.06 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.693 r_dihedral_angle_4_deg 16.743 r_dihedral_angle_3_deg 12.954 r_long_range_B_refined 5.561 r_dihedral_angle_1_deg 5.382 r_scbond_it 2.674 r_angle_refined_deg 1.706 r_mcangle_it 1.581 r_mcbond_it 1.049 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.693 r_dihedral_angle_4_deg 16.743 r_dihedral_angle_3_deg 12.954 r_long_range_B_refined 5.561 r_dihedral_angle_1_deg 5.382 r_scbond_it 2.674 r_angle_refined_deg 1.706 r_mcangle_it 1.581 r_mcbond_it 1.049 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3515 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 3
Software Software Software Name Purpose Auto-Rickshaw phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling