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dTDP-MANGANESE COMPLEX OF SPSA FROM BACILLUS SUBTILIS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QGQ PDB ENTRY 1QGQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 15% PEG 8000, 100MM HEPES BUFFER PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.04 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.372 α = 90 b = 142.06 β = 90 c = 81.425 γ = 90
Symmetry Space Group C 2 2 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 ADSC CCD 1998-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2 25.8 99.3 0.087 11.8 4.5 17948
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 2 2.07 100 0.28 4 4.5
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 PDB ENTRY 1QGQ 2 20 17948 923 99.3 0.193 0.191 0.2025 0.237 0.2378 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.142 r_scbond_it 2.438 r_angle_other_deg 1.68 r_dihedral_angle_3_deg 1.522 r_mcangle_it 1.501 r_symmetry_hbond_refined 1.118 r_mcbond_it 0.79 r_nbd_refined 0.226 r_nbd_other 0.218 r_symmetry_vdw_other 0.2
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.142 r_scbond_it 2.438 r_angle_other_deg 1.68 r_dihedral_angle_3_deg 1.522 r_mcangle_it 1.501 r_symmetry_hbond_refined 1.118 r_mcbond_it 0.79 r_nbd_refined 0.226 r_nbd_other 0.218 r_symmetry_vdw_other 0.2 r_metal_ion_refined 0.159 r_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_other 0.128 r_chiral_restr 0.1 r_symmetry_vdw_refined 0.091 r_nbtor_other 0.041 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1984 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing