☰ Navigation Tabs
Structure of the wild-type TCP10 domain of Danio rerio CPAP in complex with a peptide of Danio rerio STIL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BXP PDB ENTRY 4BXP (DISTORTED)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100 MM TRIS PH 8.5, 200 MM CA ACETATE, 17% PEG-2000 MME
Crystal Properties Matthews coefficient Solvent content 2.39 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.25 α = 90 b = 67.47 β = 113.92 c = 61.65 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 PIXEL DECTRIS PIXEL 2012-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.2 56.4 99.9 0.1 7.6 4.8 23051 1.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.9 1.01 1.4 4.9
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 PDB ENTRY 4BXP (DISTORTED) 2.2 51.13 21892 1145 99.83 0.23642 0.23427 0.2367 0.27668 0.2809 RANDOM 59.692
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] 1.66 -0.74 -2.75 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 18.937 r_dihedral_angle_3_deg 15.434 r_mcangle_it 7.864 r_dihedral_angle_1_deg 6.613 r_mcbond_it 5.311 r_angle_refined_deg 1.619 r_mcbond_other 1.418 r_angle_other_deg 1.149 r_xyhbond_nbd_other 0.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 18.937 r_dihedral_angle_3_deg 15.434 r_mcangle_it 7.864 r_dihedral_angle_1_deg 6.613 r_mcbond_it 5.311 r_angle_refined_deg 1.619 r_mcbond_other 1.418 r_angle_other_deg 1.149 r_xyhbond_nbd_other 0.261 r_nbd_refined 0.238 r_symmetry_vdw_other 0.225 r_symmetry_vdw_refined 0.219 r_symmetry_hbond_refined 0.215 r_nbd_other 0.207 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.182 r_nbtor_other 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3115 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing