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Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.259 α = 90 b = 59.307 β = 90 c = 199.111 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 ADSC QUANTUM 4 2004-06-25 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.98046 APS 14-BM-D 2 SYNCHROTRON APS BEAMLINE 14-BM-D 0.98032 APS 14-BM-D 3 SYNCHROTRON APS BEAMLINE 14-BM-D 0.96480 APS 14-BM-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.01 80 98.1 0.071 0.071 8.5 6.6 43764 42938 13.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 97.8 0.201 0.201 6.05 5.5 4188
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT none 2.01 36.68 43764 42938 1292 98.1 0.198 0.198 0.204 0.243 0.2498 RANDOM 28.1
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] -3.66 7.27 -3.62
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.09 c_scbond_it 2.15 c_mcangle_it 2.05 c_mcbond_it 1.35 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4910 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 32
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing ARP/wARP model building