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Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris Bound to 1,3-dimethylurea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 23% PEG 1500, 100 mM Na Cacodylate, 10 mM N,N'-dimethylurea, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.14 70.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.106 α = 90 b = 110.106 β = 90 c = 84.872 γ = 120
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 2009-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
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 2.4 50 99.5 0.091 8.5 10.8 22979
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 2.4 2.44 97.6 0.915 6.8 1138
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 MOLECULAR REPLACEMENT THROUGHOUT 3K3F 2.4 27.47 22964 22964 1166 99.61 0.187 0.187 0.186 0.1883 0.214 0.2194 RANDOM 44.871
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] 0.45 0.22 0.45 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.846 r_dihedral_angle_4_deg 21.68 r_dihedral_angle_3_deg 15.737 r_dihedral_angle_1_deg 5.49 r_scangle_it 2.101 r_scbond_it 1.468 r_angle_refined_deg 1.338 r_mcangle_it 0.985 r_mcbond_it 0.559 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.846 r_dihedral_angle_4_deg 21.68 r_dihedral_angle_3_deg 15.737 r_dihedral_angle_1_deg 5.49 r_scangle_it 2.101 r_scbond_it 1.468 r_angle_refined_deg 1.338 r_mcangle_it 0.985 r_mcbond_it 0.559 r_nbtor_refined 0.309 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2481 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 21
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection