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Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EAE pdb entry 3EAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 291 2.5 M ammonium sulfate, 0.1 M sodium acetate, peptide ligand was added at 0.005 M concentration, pH 4.6, vapor diffusion, temperature 291K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.527 α = 90 b = 41.681 β = 90 c = 156.749 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 ADSC QUANTUM 210 2009-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97800 CHESS A1
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 1.94 25 99.9 0.039 23.4 6.4 21026
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 1.94 1.97 98.3 0.182 5.4 1039
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 3EAE 1.95 20 20561 1055 99.651 0.218 0.2164 0.2201 0.2528 0.2561 THIN SHELLS (sftools) 33.681
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] 1.07 0.167 -1.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.319 r_dihedral_angle_4_deg 20.489 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 7.048 r_scangle_it 2.547 r_scbond_it 1.658 r_angle_refined_deg 1.21 r_mcangle_it 1.048 r_mcbond_it 0.611 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.319 r_dihedral_angle_4_deg 20.489 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 7.048 r_scangle_it 2.547 r_scbond_it 1.658 r_angle_refined_deg 1.21 r_mcangle_it 1.048 r_mcbond_it 0.611 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2034 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction