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Crystal Structure of Longer Splice Variant of PTD012 from Homo sapiens reveals a novel Zinc-containing fold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other NIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 25% PEG4000, 200mm ammonium acetate, 12% Glycerol, 100mm Na-acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.572 α = 90 b = 52.888 β = 88.89 c = 124.485 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 IMAGE PLATE MARRESEARCH mirrors 2004-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.7 20 95.6 0.055 0.055 22.2 3.7 228515 61064 22
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) 1 1.7 1.74 95.7 0.215 0.215 6.8 3.6 4018
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NIL 1.7 20 57927 3103 95.56 0.18987 0.1981 0.22159 0.2283 RANDOM 22.891
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] -1.57 0.52 0.65 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.003 r_dihedral_angle_4_deg 14.247 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 8.072 r_scangle_it 2.281 r_scbond_it 1.619 r_angle_refined_deg 1.31 r_angle_other_deg 1.235 r_mcangle_it 0.918 r_mcbond_it 0.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.003 r_dihedral_angle_4_deg 14.247 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 8.072 r_scangle_it 2.281 r_scbond_it 1.619 r_angle_refined_deg 1.31 r_angle_other_deg 1.235 r_mcangle_it 0.918 r_mcbond_it 0.669 r_nbd_refined 0.195 r_symmetry_vdw_other 0.185 r_nbd_other 0.183 r_nbtor_refined 0.174 r_mcbond_other 0.155 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.087 r_nbtor_other 0.084 r_metal_ion_refined 0.031 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4846 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing