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Crystal structure of the second RRM domain of human PABPC1 at pH 6.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 25% PEG 1500 and 0.1 M MIB buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.85 33.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.653 α = 90 b = 50.653 β = 90 c = 63.447 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 210 2007-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9772 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 97.7 0.077 16.9 9.5 7363 7194 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 82.7 0.279 5.3 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1cvj 1.9 19.05 1 7363 7194 345 97.63 0.22 0.21915 0.21663 0.2159 0.26919 0.2625 RANDOM 39.49
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] -0.09 -0.04 -0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.614 r_dihedral_angle_4_deg 25.628 r_dihedral_angle_3_deg 19.082 r_dihedral_angle_1_deg 6.347 r_scangle_it 2.632 r_scbond_it 1.678 r_angle_refined_deg 1.218 r_mcangle_it 1.203 r_mcbond_it 0.665 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.614 r_dihedral_angle_4_deg 25.628 r_dihedral_angle_3_deg 19.082 r_dihedral_angle_1_deg 6.347 r_scangle_it 2.632 r_scbond_it 1.678 r_angle_refined_deg 1.218 r_mcangle_it 1.203 r_mcbond_it 0.665 r_nbtor_refined 0.304 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.159 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 623 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling