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Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.83 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 40.0% 1,2-propanediol, 0.05M calcium acetate, 0.1M acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.06 40.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.904 α = 90 b = 52.481 β = 95.59 c = 85.462 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 325 mm CCD double crystal monochromator 2005-03-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.89194,0.97946,0.97929 SSRL BL9-2
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 1.83 44.677 100 0.094 0.094 8.2 3.7 42195
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 1.83 1.93 100 0.552 0.552 2.4 3.7 6174
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.83 44.677 42154 2116 99.97 0.1564 0.1545 0.1605 0.1928 0.1964 RANDOM 25.1014
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] -0.8 -0.01 -0.38 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.897 r_dihedral_angle_4_deg 17.844 r_dihedral_angle_3_deg 13.512 r_scangle_it 8.161 r_dihedral_angle_1_deg 5.958 r_scbond_it 5.239 r_mcangle_it 2.822 r_mcbond_it 1.708 r_angle_refined_deg 1.432 r_angle_other_deg 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.897 r_dihedral_angle_4_deg 17.844 r_dihedral_angle_3_deg 13.512 r_scangle_it 8.161 r_dihedral_angle_1_deg 5.958 r_scbond_it 5.239 r_mcangle_it 2.822 r_mcbond_it 1.708 r_angle_refined_deg 1.432 r_angle_other_deg 0.899 r_mcbond_other 0.593 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3978 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 48
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing SCALA data scaling REFMAC refinement XDS data reduction XSCALE data scaling SHELXD phasing autoSHARP phasing