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Crystal structure of deoxyribose phosphate aldolase from mycobacterium avium 104 in a schiff base with an unknown aldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J2W PDB ENTRY 1J2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 JCSG SCREEN CONDITION H3: 100MM BIS-TRIS PH 5.5, 25% PEG 3350; PROTEIN AT 60 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.91 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.48 α = 90 b = 116.32 β = 105.76 c = 101.28 γ = 90
Symmetry Space Group C 1 2 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 315 2010-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.15 44.78 91.3 0.043 23.03 4.2 54848 50086 -3 27.73
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 2.15 2.21 95.8 0.157 7.9 4.06 4051
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR, MR THROUGHOUT PDB ENTRY 1J2W 2.15 44.78 50052 2530 0.188 0.186 0.228 0.2259 RANDOM 21.725
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] -0.25 -0.01 0.21 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 11.666 r_dihedral_angle_1_deg 6.271 r_scangle_it 2.973 r_scbond_it 1.859 r_angle_refined_deg 1.362 r_mcangle_it 1.066 r_angle_other_deg 0.909 r_mcbond_it 0.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 11.666 r_dihedral_angle_1_deg 6.271 r_scangle_it 2.973 r_scbond_it 1.859 r_angle_refined_deg 1.362 r_mcangle_it 1.066 r_angle_other_deg 0.909 r_mcbond_it 0.619 r_mcbond_other 0.17 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5948 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 41
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling