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Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 25.0% 1,2-propanediol, 10.0% Glycerol, 5.0% PEG-3000, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.812 α = 90 b = 51.818 β = 95.23 c = 84.735 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 ADSC QUANTUM 4 FLAT MIRROR 2002-03-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.918370,0.977757 SSRL BL9-1
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 1.75 47.226 86.2 0.087 10.91 3.56 40637 -3 16.819
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 1.75 1.81 33.7 0.527 1.5
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 1.75 47.226 40622 2046 86.17 0.1548 0.1529 0.1592 0.1915 0.1927 RANDOM 22.0715
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] -0.56 -0.56 -1.32 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.626 r_dihedral_angle_4_deg 15.687 r_dihedral_angle_3_deg 13.089 r_scangle_it 7.111 r_dihedral_angle_1_deg 6.137 r_scbond_it 4.878 r_mcangle_it 2.511 r_mcbond_it 1.573 r_angle_refined_deg 1.38 r_angle_other_deg 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.626 r_dihedral_angle_4_deg 15.687 r_dihedral_angle_3_deg 13.089 r_scangle_it 7.111 r_dihedral_angle_1_deg 6.137 r_scbond_it 4.878 r_mcangle_it 2.511 r_mcbond_it 1.573 r_angle_refined_deg 1.38 r_angle_other_deg 0.881 r_mcbond_other 0.473 r_chiral_restr 0.08 r_bond_refined_d 0.015 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 3928 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 37
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing autoSHARP phasing