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A novel conformation for the TPR domain of pex5p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C0M PDB ENTRY 2C0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.75 23% (W/V) PEG 3350, 100 MM TRIS-HCL (PH 8.75) AND 10 MM SRCL2
Crystal Properties Matthews coefficient Solvent content 2.35 39.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.67 α = 90 b = 91.41 β = 90 c = 119.89 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2004-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.65 20 93.5 0.1 11.7 3.8 16659 -3
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 2.65 2.8 95.3 0.58 2.5 3.8
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 2C0M 2.65 20 15824 834 93.8 0.244 0.241 0.239 0.3 0.2939 RANDOM 37.35
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] 0.11 1.45 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.909 r_dihedral_angle_3_deg 17.283 r_dihedral_angle_4_deg 13.863 r_dihedral_angle_1_deg 5.225 r_scangle_it 0.946 r_angle_refined_deg 0.876 r_angle_other_deg 0.81 r_scbond_it 0.598 r_mcangle_it 0.481 r_mcbond_it 0.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.909 r_dihedral_angle_3_deg 17.283 r_dihedral_angle_4_deg 13.863 r_dihedral_angle_1_deg 5.225 r_scangle_it 0.946 r_angle_refined_deg 0.876 r_angle_other_deg 0.81 r_scbond_it 0.598 r_mcangle_it 0.481 r_mcbond_it 0.261 r_nbd_refined 0.198 r_nbtor_refined 0.174 r_nbd_other 0.16 r_symmetry_vdw_refined 0.155 r_symmetry_vdw_other 0.132 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.111 r_nbtor_other 0.083 r_chiral_restr 0.049 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 4445 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing