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The X-ray crystal structure of SSR4, an S. pombe chromatin remodelling protein: sulfur SAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 Crystallisation experiments were set up in SD2 sitting drop plates at 8 C with 200 nL protein plus 200 nL reservoir with 50 uL of reservoir in the wells. The protein concentration was 5 mg/mL. Reservoir conditions contained 1.5 to 1.9 M ammonium sulfate, 0.7-12% dioxane and either 100 mM MES, 100 mM bis-tris or 10% (v/v) malate-MES-tris buffer at a pH between 5.5 and 5.8
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.342 α = 90 b = 68.255 β = 90 c = 67.779 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 315 2013-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.548600 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 40.4 99.9 0.355 0.036 0.999 18.3 97.3 14204
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 99.6 0.469 0.753 1.7 101
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7k7v 2.1 40.4 14158 590 99.944 0.193 0.1917 0.2003 0.2217 0.231 38.082
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] 1.635 -0.465 -1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.186 r_dihedral_angle_4_deg 22.305 r_dihedral_angle_3_deg 13.019 r_lrange_it 8.733 r_lrange_other 8.72 r_dihedral_angle_1_deg 7.287 r_scangle_it 6.325 r_scangle_other 6.322 r_mcangle_it 4.492 r_mcangle_other 4.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.186 r_dihedral_angle_4_deg 22.305 r_dihedral_angle_3_deg 13.019 r_lrange_it 8.733 r_lrange_other 8.72 r_dihedral_angle_1_deg 7.287 r_scangle_it 6.325 r_scangle_other 6.322 r_mcangle_it 4.492 r_mcangle_other 4.49 r_scbond_it 4.135 r_scbond_other 4.133 r_mcbond_it 3.195 r_mcbond_other 3.189 r_angle_refined_deg 1.534 r_angle_other_deg 1.265 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_refined 0.193 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.168 r_nbd_other 0.159 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.137 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1519 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing