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Putative sugar aminotransferase Spr1654 from Streptococcus pneumoniae, apo-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.2 M Sodium acetate trihydrate
0.1 M Sodium cacodylate trihydrate pH 6.5
30% w/v Polyethylene glycol 8 000
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.33 α = 90 b = 99.982 β = 97.66 c = 110.422 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 PIXEL DECTRIS PILATUS3 2M 2015-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97 ESRF ID30B
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 1.9 30 97 0.063 10.9 2.7 130980
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 1.9 2 0.444 2.3
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 4LC3 1.9 30 130980 6467 97 0.238 0.236 0.2403 0.265 0.2678 RANDOM 28.3
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] -0.09 0.04 -0.06 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.034 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 6.335 r_long_range_B_refined 3.887 r_long_range_B_other 3.794 r_angle_refined_deg 1.572 r_angle_other_deg 1.371 r_scangle_other 1.146 r_mcangle_it 1.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.034 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_1_deg 6.335 r_long_range_B_refined 3.887 r_long_range_B_other 3.794 r_angle_refined_deg 1.572 r_angle_other_deg 1.371 r_scangle_other 1.146 r_mcangle_it 1.081 r_mcangle_other 1.081 r_scbond_it 0.7 r_scbond_other 0.7 r_mcbond_it 0.646 r_mcbond_other 0.646 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12564 Nucleic Acid Atoms Solvent Atoms 713 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing