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The crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M Bis-tris,
0.2M Na(OAc),
30% PEG 8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.651 α = 90 b = 66.83 β = 108.19 c = 69.967 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 SBC-3 mirror 2008-01-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97929, 0.97942 APS 19-BM
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 1.94 30 99.7 0.083 22.8 4.3 34554 34554
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 1.95 2.01 98.7 0.608 1.67 3.8 2833
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.94 29.76 32787 32787 1726 99.26 0.18928 0.18928 0.1867 0.23804 0.2691 RANDOM 41.966
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] -0.28 0.05 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.643 r_dihedral_angle_3_deg 18.304 r_dihedral_angle_4_deg 17.215 r_dihedral_angle_1_deg 6.506 r_scangle_it 3.304 r_scbond_it 2.216 r_angle_refined_deg 1.647 r_mcangle_it 1.316 r_mcbond_it 0.82 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.643 r_dihedral_angle_3_deg 18.304 r_dihedral_angle_4_deg 17.215 r_dihedral_angle_1_deg 6.506 r_scangle_it 3.304 r_scbond_it 2.216 r_angle_refined_deg 1.647 r_mcangle_it 1.316 r_mcbond_it 0.82 r_nbtor_refined 0.309 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.216 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.123 r_bond_refined_d 0.016 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 3541 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXD phasing MLPHARE phasing DM phasing RESOLVE phasing HKL-3000 phasing