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The X-ray crystal structure of SSR4, an S. pombe chromatin remodelling protein: native
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 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.096 α = 90 b = 67.506 β = 90 c = 67.463 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 0.911684 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 1.77 47.7 100 0.169 0.047 0.998 10.9 13.5 23002
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 1.77 1.81 100 0.893 0.423 1.1 8
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 1.77 47.7 22947 1090 99.97 0.178 0.1768 0.189 0.2056 0.2127 21.738
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] -0.593 1.108 -0.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.199 r_dihedral_angle_4_deg 15.807 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_1_deg 6.862 r_lrange_it 6.19 r_lrange_other 6.134 r_scangle_it 5.088 r_scangle_other 5.086 r_scbond_it 3.309 r_scbond_other 3.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.199 r_dihedral_angle_4_deg 15.807 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_1_deg 6.862 r_lrange_it 6.19 r_lrange_other 6.134 r_scangle_it 5.088 r_scangle_other 5.086 r_scbond_it 3.309 r_scbond_other 3.308 r_mcangle_it 3.064 r_mcangle_other 3.064 r_mcbond_it 2.142 r_mcbond_other 2.128 r_angle_refined_deg 1.632 r_angle_other_deg 1.433 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.21 r_symmetry_nbd_other 0.19 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.174 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1505 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing