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Structure of the E1021V mutant of the TCP10 domain of Danio rerio CPAP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BXP PDB ENTRY 4BXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 80 MM TRIS PH 8.5, 160 MM MGCL2, 24% PEG-4000, 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.12 α = 90 b = 36.48 β = 117.47 c = 56.46 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 MAR scanner 345 mm plate MULTILAYER FOCUSSING OPTICS 2010-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 1.9 36.5 100 0.1 13.8 6.8 15136 1.8
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 1.9 2 100 1.09 1.8 6.6
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 1.9 29.49 14349 762 99.88 0.21212 0.20913 0.2122 0.26682 0.2693 RANDOM 31.553
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] 1.29 -0.06 0.89 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.357 r_dihedral_angle_4_deg 24.411 r_dihedral_angle_3_deg 13.071 r_dihedral_angle_1_deg 5.267 r_scangle_it 3.747 r_mcangle_it 3.36 r_scbond_it 2.295 r_mcbond_other 2.036 r_mcbond_it 2.035 r_angle_refined_deg 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.357 r_dihedral_angle_4_deg 24.411 r_dihedral_angle_3_deg 13.071 r_dihedral_angle_1_deg 5.267 r_scangle_it 3.747 r_mcangle_it 3.36 r_scbond_it 2.295 r_mcbond_other 2.036 r_mcbond_it 2.035 r_angle_refined_deg 1.31 r_angle_other_deg 0.718 r_nbd_refined 0.251 r_symmetry_vdw_refined 0.206 r_symmetry_hbond_refined 0.189 r_nbd_other 0.182 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_other 0.16 r_nbtor_other 0.077 r_chiral_restr 0.073 r_xyhbond_nbd_other 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_other 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 1372 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing