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Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 20.025% PEG 8000, 0.08M HEPES, 0.02M HEPES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.02 38.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.997 α = 90 b = 64.848 β = 100.92 c = 77.427 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 ADSC 2003-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 50 95.39 0.051 19.88 2.56 44165 20.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 71.07 0.303 2.4 1.76 3277
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 1VJF 1.6 49.34 41937 2209 100 0.15366 0.15201 0.167 0.18496 0.2011 RANDOM 10.51
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] 0.43 -0.57 -0.43 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_4_deg 16.524 r_dihedral_angle_3_deg 9.978 r_scangle_it 6.451 r_dihedral_angle_1_deg 5.675 r_scbond_it 4.59 r_mcangle_it 2.63 r_mcbond_it 2.22 r_angle_refined_deg 1.497 r_angle_other_deg 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_4_deg 16.524 r_dihedral_angle_3_deg 9.978 r_scangle_it 6.451 r_dihedral_angle_1_deg 5.675 r_scbond_it 4.59 r_mcangle_it 2.63 r_mcbond_it 2.22 r_angle_refined_deg 1.497 r_angle_other_deg 0.835 r_mcbond_other 0.581 r_symmetry_vdw_other 0.236 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.203 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_refined 0.108 r_chiral_restr 0.096 r_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2550 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement