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Crystal structure of CerJ from Streptomyces tendae - malonic acid covalently linked to the catalytic Cystein C116
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 22.5% PEG 4000,
100 mM Tris/HCl pH 8.5,
200 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.04 α = 90 b = 106.04 β = 90 c = 121.69 γ = 90
Symmetry Space Group P 41 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 MARMOSAIC 225 mm CCD 2010-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.12 30 99.7 39987 39874 3 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 2.12 2.18 99.9 0.674 3.07 7.3 2916
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.12 29.41 37875 1994 100 0.16981 0.16774 0.1765 0.20816 0.2158 RANDOM 50.32
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] 1.52 1.52 -3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.818 r_dihedral_angle_4_deg 16.863 r_dihedral_angle_3_deg 15.221 r_dihedral_angle_1_deg 12.504 r_scangle_it 3.874 r_scbond_it 2.959 r_mcangle_it 2.662 r_mcbond_it 2.019 r_angle_refined_deg 1.571 r_angle_other_deg 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.818 r_dihedral_angle_4_deg 16.863 r_dihedral_angle_3_deg 15.221 r_dihedral_angle_1_deg 12.504 r_scangle_it 3.874 r_scbond_it 2.959 r_mcangle_it 2.662 r_mcbond_it 2.019 r_angle_refined_deg 1.571 r_angle_other_deg 0.964 r_mcbond_other 0.853 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 5036 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing