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Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.04 293 0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.413 α = 90 b = 59.386 β = 90 c = 169.212 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 2010-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.9796 BSRF 3W1A
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 1.9 20 89.5 0.109 26.5 11.2 39859
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 1.9 1.93 78.8 0.432 4.2 10.2
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 (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 2HVY 1.9 19.92 37603 1971 89.7 0.20509 0.20355 0.2036 0.23343 0.2341 RANDOM 27.503
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] -0.7 0.11 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.657 r_dihedral_angle_4_deg 18.301 r_dihedral_angle_3_deg 16.797 r_dihedral_angle_1_deg 6.038 r_scangle_it 3.352 r_scbond_it 1.976 r_mcangle_it 1.548 r_angle_refined_deg 1.314 r_mcbond_it 0.865 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.657 r_dihedral_angle_4_deg 18.301 r_dihedral_angle_3_deg 16.797 r_dihedral_angle_1_deg 6.038 r_scangle_it 3.352 r_scbond_it 1.976 r_mcangle_it 1.548 r_angle_refined_deg 1.314 r_mcbond_it 0.865 r_chiral_restr 0.103 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3749 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling