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Crystal structure of apo-SpuD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 25% PEG 3350, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.769 α = 90 b = 108.983 β = 90 c = 228.508 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 IMAGE PLATE RIGAKU 2009-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 20 84.9 23272 23272 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 80.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3TTM 2.97 20 2 20613 20613 1086 85.26 0.21876 0.21876 0.21517 0.28794 0.2471 RANDOM 39.859
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] 3.42 -1.52 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.911 r_dihedral_angle_3_deg 18.25 r_dihedral_angle_4_deg 17.061 r_dihedral_angle_1_deg 5.314 r_angle_refined_deg 1.207 r_scangle_it 1.055 r_mcangle_it 0.65 r_scbond_it 0.592 r_mcbond_it 0.35 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.911 r_dihedral_angle_3_deg 18.25 r_dihedral_angle_4_deg 17.061 r_dihedral_angle_1_deg 5.314 r_angle_refined_deg 1.207 r_scangle_it 1.055 r_mcangle_it 0.65 r_scbond_it 0.592 r_mcbond_it 0.35 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8025 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction PHASER phasing REFMAC refinement SCALA data scaling