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SyrB2 with Fe(II), bromide, and alpha-ketoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SyrB2 with Fe(II), chloride, and alpha-ketoglutarate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 15% PEG 3350, 250 mM Na formate, spermine tetra-HCl, n-decanoyl sucrose , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.12 α = 90 b = 89.35 β = 90 c = 125.06 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH double crystal monochromator 2005-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9195 SSRL BL9-2
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 1.8 42.18 95.3 0.072 18.2 7.6 57215 57215 17.2
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 1.8 1.9 86.4 0.337 2.4 5.9 7474
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION RIGID BODY THROUGHOUT SyrB2 with Fe(II), chloride, and alpha-ketoglutarate 1.8 42.18 56498 56498 3341 93.98 0.173 0.173 0.171 0.1801 0.21 0.2166 Same as starting model 17.096
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] -0.23 -0.11 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.644 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_4_deg 13.923 r_dihedral_angle_1_deg 6.836 r_scangle_it 3.437 r_scbond_it 2.474 r_mcangle_it 1.535 r_angle_refined_deg 1.532 r_mcbond_it 1.387 r_angle_other_deg 1.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.644 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_4_deg 13.923 r_dihedral_angle_1_deg 6.836 r_scangle_it 3.437 r_scbond_it 2.474 r_mcangle_it 1.535 r_angle_refined_deg 1.532 r_mcbond_it 1.387 r_angle_other_deg 1.345 r_symmetry_vdw_other 0.282 r_mcbond_other 0.252 r_nbd_refined 0.208 r_nbd_other 0.203 r_nbtor_refined 0.187 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.097 r_nbtor_other 0.089 r_bond_refined_d 0.015 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 4814 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 60
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling CNS phasing