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Crystal structure of malonate occupied DctB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E4P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 289 0.2 M SODIUM MALONATE PH 6.0, 13-15% PEG 3350, 5-10 mM STRONTIUM CHLORIDE, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.91 35.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.98 α = 90 b = 39.1 β = 94.78 c = 111.54 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 MAR CCD 165 mm 2007-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A BSRF 3W1A
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 2.3 30.5 97.5 0.069 12.12 22061 -3 39.49
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 2.3 2.4 94.7 0.389 2.7
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 PDB 3E4P 2.3 30 20919 1142 97.6 0.199 0.196 0.2038 0.262 0.262 RANDOM 33.02
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] -0.09 0.02 2.28 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.582 r_dihedral_angle_4_deg 19.186 r_dihedral_angle_3_deg 17.027 r_dihedral_angle_1_deg 7.974 r_scangle_it 3.544 r_scbond_it 2.198 r_angle_refined_deg 1.664 r_mcangle_it 1.256 r_mcbond_it 0.677 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.582 r_dihedral_angle_4_deg 19.186 r_dihedral_angle_3_deg 17.027 r_dihedral_angle_1_deg 7.974 r_scangle_it 3.544 r_scbond_it 2.198 r_angle_refined_deg 1.664 r_mcangle_it 1.256 r_mcbond_it 0.677 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.269 r_xyhbond_nbd_refined 0.249 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.212 r_chiral_restr 0.11 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_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3854 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 17
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling