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Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N1-(2.3-dihydro-1H-inden-5-yl)acetam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M AMMONIUM ACETATE, 0.1M BIS:TRIS:HCL, PH 6.5, 25% PEG335, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.253 α = 90 b = 81.199 β = 98.45 c = 82.922 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 QUANTUM 315 2013-03-28 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.7 50 97.4 0.098 8.8 3.6 72142
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 1.7 1.73 78.8 0.423 3
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 4E3A 1.7 40.2 68385 3641 97.5 0.16781 0.16518 0.162 0.21762 0.2128 RANDOM 29.619
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] -0.08 -0.18 -0.03 0.11
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.317 r_dihedral_angle_2_deg 37.569 r_sphericity_bonded 18.921 r_dihedral_angle_4_deg 13.38 r_dihedral_angle_3_deg 13.16 r_dihedral_angle_1_deg 5.649 r_rigid_bond_restr 2.381 r_angle_refined_deg 1.32 r_chiral_restr 0.081 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.317 r_dihedral_angle_2_deg 37.569 r_sphericity_bonded 18.921 r_dihedral_angle_4_deg 13.38 r_dihedral_angle_3_deg 13.16 r_dihedral_angle_1_deg 5.649 r_rigid_bond_restr 2.381 r_angle_refined_deg 1.32 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5008 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 82
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction