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Crystal Structure of Profilin from Schizosaccharomyces pombe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ACG PDB ENTRY 2ACG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 1.3 M Na Malonate; 0.2 M Hepes pH 7.0; 0.5% JeffamineED2001 [O O'-BIS (2-aminopropyl) polyethylene glycol 1900] from Hampton Research], VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.533 α = 90 b = 84.021 β = 93.73 c = 40.42 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 273 IMAGE PLATE MAR scanner 345 mm plate 2006-10-02 M SINGLE WAVELENGTH 2 1 x-ray CCD MARRESEARCH 2007-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 200 1.54178 2 SYNCHROTRON NSLS BEAMLINE X29A 1.08090 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1,2 1.65 50 92 0.039 0.048 19.3 2.8 59358 24741
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.65 1.81 73.3 0.256 0.17 2.23 1.9 1783
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 (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 PDB ENTRY 2ACG 1.65 42 24740 1262 84.86 0.177 0.177 0.175 0.2299 0.206 0.2497 RANDOM 15.225
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] 1.78 -0.85 -1.37 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.257 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_4_deg 14.438 r_dihedral_angle_1_deg 5.045 r_scangle_it 2.127 r_scbond_it 1.515 r_angle_refined_deg 1.255 r_mcangle_it 0.856 r_angle_other_deg 0.816 r_mcbond_it 0.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.257 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_4_deg 14.438 r_dihedral_angle_1_deg 5.045 r_scangle_it 2.127 r_scbond_it 1.515 r_angle_refined_deg 1.255 r_mcangle_it 0.856 r_angle_other_deg 0.816 r_mcbond_it 0.656 r_symmetry_hbond_refined 0.442 r_chiral_restr 0.252 r_nbd_refined 0.205 r_nbtor_refined 0.178 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.166 r_mcbond_other 0.141 r_symmetry_vdw_refined 0.127 r_symmetry_vdw_other 0.085 r_nbtor_other 0.08 r_symmetry_hbond_other 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1866 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection