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Crystal structure of uncharacterized protein ATU2773 from Agrobacterium tumefaciens C58
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NLY PDB entry 2NLY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 100mM Sodium cacodylate pH 6.5, 400mM Sodium acetate pH 4.6, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.349 α = 91.06 b = 47.373 β = 92.36 c = 65.492 γ = 73.06
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 2007-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 50 97.7 0.114 0.104 4.2 2 33092 -0.5 19.439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 96.6 0.75 0.78 0.9 2
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 entry 2NLY 1.9 20 31951 1037 97.28 0.17978 0.17786 0.1783 0.23838 0.2377 RANDOM 24.503
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] 0.33 -0.64 -0.21 0.4 0.37 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_3_deg 14.323 r_dihedral_angle_4_deg 14.085 r_scangle_it 8.375 r_scbond_it 5.79 r_dihedral_angle_1_deg 5.323 r_mcangle_it 4.351 r_mcbond_it 3.289 r_angle_refined_deg 1.291 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.431 r_dihedral_angle_3_deg 14.323 r_dihedral_angle_4_deg 14.085 r_scangle_it 8.375 r_scbond_it 5.79 r_dihedral_angle_1_deg 5.323 r_mcangle_it 4.351 r_mcbond_it 3.289 r_angle_refined_deg 1.291 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.165 r_nbd_refined 0.151 r_symmetry_vdw_refined 0.101 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 3662 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 6
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling