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Crystal Structure of Human PABPN1 RRM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B4D PDB ENTRY 3B4D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283 0.1M HEPES, 4.2M sodium chloride, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 1.89 34.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.338 α = 90 b = 59.338 β = 90 c = 80.599 γ = 120
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 2007-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.9800 BSRF 3W1A
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 2.816 80.582 0.063 8.4 7694
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.816 2.92
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 3B4D 2.82 80.58 7338 354 99.88 0.22932 0.22631 0.2309 0.2897 0.2887 RANDOM 37.295
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] 1.1 0.55 1.1 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.991 r_dihedral_angle_4_deg 23.039 r_dihedral_angle_3_deg 17.844 r_dihedral_angle_1_deg 5.966 r_scangle_it 2.111 r_scbond_it 1.394 r_angle_refined_deg 1.252 r_mcangle_it 0.989 r_mcbond_it 0.65 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.991 r_dihedral_angle_4_deg 23.039 r_dihedral_angle_3_deg 17.844 r_dihedral_angle_1_deg 5.966 r_scangle_it 2.111 r_scbond_it 1.394 r_angle_refined_deg 1.252 r_mcangle_it 0.989 r_mcbond_it 0.65 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.27 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 2489 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction MOLREP phasing