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The crystal structure of PDEd in complex with inhibitor-2a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Calcium acetate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.51 50.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.76 α = 97.7 b = 40.9 β = 102.38 c = 68.8 γ = 89.31
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9786 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 26.06 97.7 0.113 9.54 3.45 9570
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 96.7 0.466 3.26 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT 3T5G 2.6 26.06 9570 504 97.81 0.1884 0.1853 0.1889 0.2473 0.2454 RANDOM 35.365
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] -0.01 -0.04 -0.02 -0.04 0.04 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.733 r_dihedral_angle_3_deg 16.239 r_dihedral_angle_4_deg 11.417 r_dihedral_angle_1_deg 7.382 r_mcangle_it 2.649 r_mcbond_it 1.669 r_mcbond_other 1.663 r_angle_refined_deg 1.474 r_angle_other_deg 0.821 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.733 r_dihedral_angle_3_deg 16.239 r_dihedral_angle_4_deg 11.417 r_dihedral_angle_1_deg 7.382 r_mcangle_it 2.649 r_mcbond_it 1.669 r_mcbond_other 1.663 r_angle_refined_deg 1.474 r_angle_other_deg 0.821 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2424 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 64
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement Coot model building