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Crystal structure of yeast SmF in spacegroup P43212
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N9R PDB ID: 1N9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 Tris, PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.635 α = 90 b = 105.635 β = 90 c = 235.563 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 AREA DETECTOR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.000 SSRL BL9-2
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 3.5 95 99.3 0.064 23.5 6.7 16292 88.9
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 3.5 3.69 99.3 0.381 6 6.8
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-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 ID: 1N9R 3.5 20 16292 876 98.41 0.29193 0.29193 0.29167 0.2593 0.29683 0.2604 RANDOM 44.801
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] 8.05 8.05 -16.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.23 r_dihedral_angle_1_deg 5.003 r_scangle_it 3.383 r_angle_refined_deg 2.282 r_scbond_it 1.879 r_mcangle_it 1.636 r_angle_other_deg 1.332 r_mcbond_it 0.851 r_symmetry_hbond_refined 0.659 r_symmetry_vdw_refined 0.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.23 r_dihedral_angle_1_deg 5.003 r_scangle_it 3.383 r_angle_refined_deg 2.282 r_scbond_it 1.879 r_mcangle_it 1.636 r_angle_other_deg 1.332 r_mcbond_it 0.851 r_symmetry_hbond_refined 0.659 r_symmetry_vdw_refined 0.445 r_symmetry_vdw_other 0.42 r_nbd_refined 0.295 r_nbd_other 0.278 r_xyhbond_nbd_refined 0.258 r_xyhbond_nbd_other 0.166 r_chiral_restr 0.13 r_nbtor_other 0.108 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7887 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling