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PdxS (G. stearothermophilus) co-crystallized with R5P in the presence of ammonia.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 8000, Na cacodylate, ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.68 α = 90 b = 107.198 β = 92.24 c = 178.215 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 MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors 2012-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
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 2.3 50 100 0.093 9.6 3.8 158883
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 2.3 2.38 100 0.74 3.8 15858
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 1ZNN 2.3 50 158883 7970 99.41 0.1929 0.1913 0.1927 0.2223 0.2205 RANDOM 49.576
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] 0.4 -1.06 1.14 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.656 r_dihedral_angle_4_deg 18.782 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.338 r_mcangle_it 3.924 r_mcbond_it 2.43 r_mcbond_other 2.43 r_angle_refined_deg 1.085 r_angle_other_deg 0.739 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.656 r_dihedral_angle_4_deg 18.782 r_dihedral_angle_3_deg 12.354 r_dihedral_angle_1_deg 5.338 r_mcangle_it 3.924 r_mcbond_it 2.43 r_mcbond_other 2.43 r_angle_refined_deg 1.085 r_angle_other_deg 0.739 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22595 Nucleic Acid Atoms Solvent Atoms 1236 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction HKL-2000 data scaling