☰ Navigation Tabs
Crystal structure of Pdcd4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 20% PEG MME 2000, 0.1M Tris-HCl pH8.5, 0.2M trimethylamine N-oxide (TMAO), 10mM DTT, 10mM sarcosine, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.92 68.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.325 α = 90 b = 170.325 β = 90 c = 66.919 γ = 120
Symmetry Space Group P 31 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 2006-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9798 ESRF BM14
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 2.8 30 100 0.084 5 9.8 27711
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.8 30 27686 1394 100 0.23531 0.23531 0.2371 0.27666 0.2587 RANDOM 30.577
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] 0.62 0.31 0.62 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.367 r_dihedral_angle_3_deg 16.597 r_dihedral_angle_4_deg 16.427 r_dihedral_angle_1_deg 3.29 r_scangle_it 0.826 r_angle_refined_deg 0.806 r_scbond_it 0.465 r_mcangle_it 0.419 r_symmetry_hbond_refined 0.356 r_symmetry_vdw_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.367 r_dihedral_angle_3_deg 16.597 r_dihedral_angle_4_deg 16.427 r_dihedral_angle_1_deg 3.29 r_scangle_it 0.826 r_angle_refined_deg 0.806 r_scbond_it 0.465 r_mcangle_it 0.419 r_symmetry_hbond_refined 0.356 r_symmetry_vdw_refined 0.321 r_nbtor_refined 0.296 r_mcbond_it 0.221 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4362 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SnB phasing SHARP phasing