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Crystal Structure of KD(P)GA from T.tenax
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W3N PDB entry 1W3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 HEPES/KOH, pH 7, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.92 68.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.76 α = 90 b = 149.76 β = 90 c = 173.47 γ = 90
Symmetry Space Group P 43 21 2
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 225 mm CCD 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98 SLS X10SA
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 2.2 49.95 100 0.086 0.107 14.48 9.8 100116 100096 3 35
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) 2.2 2.5 100 0.23 0.497 5.02 10 100096
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB entry 1W3N 2.2 47.95 100094 5005 100 0.188 0.18535 0.1837 0.225 0.2214 RANDOM 34.523
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] -0.91 -0.91 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.328 r_dihedral_angle_4_deg 21.601 r_dihedral_angle_3_deg 16.097 r_dihedral_angle_1_deg 10.175 r_scangle_it 3.044 r_mcangle_it 2.717 r_scbond_it 1.936 r_angle_refined_deg 1.801 r_mcbond_it 1.717 r_symmetry_hbond_refined 0.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.328 r_dihedral_angle_4_deg 21.601 r_dihedral_angle_3_deg 16.097 r_dihedral_angle_1_deg 10.175 r_scangle_it 3.044 r_mcangle_it 2.717 r_scbond_it 1.936 r_angle_refined_deg 1.801 r_mcbond_it 1.717 r_symmetry_hbond_refined 0.762 r_nbtor_refined 0.334 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.212 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8660 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XSCALE data scaling PHASER phasing