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Crystal Structure of L. monocytogenes Pyruvate Carboxylase in complex with Cyclic-di-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 19% PEG 3350, 0.2M Ammonium Citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.13 60.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.778 α = 90 b = 153.296 β = 101.58 c = 221.24 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 CCD ADSC QUANTUM 315 MIRRORS 2013-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.5 50 97.1 0.072 15.9 3.9 209169 -3
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 2.5 2.59 87.3 0.38 3.3 3.4
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 (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 3BG5 2.51 49.8 198499 10520 96.62 0.1965 0.19454 0.2002 0.23336 0.2363 RANDOM 55.768
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] 2.93 -3.51 -4.1 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.895 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 17.523 r_dihedral_angle_1_deg 6.194 r_angle_refined_deg 1.674 r_angle_other_deg 1.083 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.895 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 17.523 r_dihedral_angle_1_deg 6.194 r_angle_refined_deg 1.674 r_angle_other_deg 1.083 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 33830 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 188
Software Software Software Name Purpose PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling