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Molecular structure of the rod domain of Dictyostelium filamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KSR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 MPD, calcium chloride, sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.06 59.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.32 α = 90 b = 61.67 β = 104.1 c = 119.03 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 100 CCD MARRESEARCH 2003-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97891 SLS X06SA
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 2.8 30 99.3 0.026 68210 20708 4 2
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) 2.8 2.85 90.1 0.124
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KSR 2.8 30 4 22012 20708 1104 99.04 0.25775 0.25746 0.26315 RANDOM 43.67
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] 2.73 -3.25 1.34 -5.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.612 r_angle_other_deg 4.038 r_angle_refined_deg 2.677 r_scangle_it 2.266 r_scbond_it 1.353 r_mcangle_it 1.123 r_mcbond_it 0.647 r_symmetry_vdw_refined 0.59 r_symmetry_vdw_other 0.568 r_symmetry_hbond_refined 0.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.612 r_angle_other_deg 4.038 r_angle_refined_deg 2.677 r_scangle_it 2.266 r_scbond_it 1.353 r_mcangle_it 1.123 r_mcbond_it 0.647 r_symmetry_vdw_refined 0.59 r_symmetry_vdw_other 0.568 r_symmetry_hbond_refined 0.343 r_nbd_other 0.305 r_nbd_refined 0.269 r_chiral_restr 0.25 r_nbtor_other 0.131 r_xyhbond_nbd_refined 0.131 r_gen_planes_refined 0.018 r_bond_refined_d 0.015 r_gen_planes_other 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4537 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing CNS phasing