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Crystal structure of putative carboxynorspermidine decarboxylase protein from Sinorhizobium meliloti
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 0.1M Bis-tris pH6.5, 0.2M Ammonium sulfate, 25% PEG3350. 1/70 subtilisin, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.06 40.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.769 α = 90 b = 75.773 β = 90 c = 129.801 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 2010-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
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 98.8 0.108 25.3 6.4 24485 24202 -3 52.2
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) 2.5 2.54 100 0.798 2.58 6.7 1183
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.5 50 24063 24063 1224 98.28 0.19362 0.19362 0.19023 0.25574 0.2309 RANDOM 47.797
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] -0.06 0.39 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 17.711 r_dihedral_angle_1_deg 6.451 r_scangle_it 3.496 r_scbond_it 2.128 r_angle_refined_deg 1.498 r_mcangle_it 1.255 r_mcbond_it 0.65 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 17.711 r_dihedral_angle_1_deg 6.451 r_scangle_it 3.496 r_scbond_it 2.128 r_angle_refined_deg 1.498 r_mcangle_it 1.255 r_mcbond_it 0.65 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5452 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 10
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM model building RESOLVE model building Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing