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Crystal structure of yeast AF-9 homolog protein Yaf9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FK3 PDB ENTRY 3FK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 26% PEG 4000, 0.1M Tris-Cl, 0.1M Guanidine Hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.643 α = 71.78 b = 44.267 β = 89.86 c = 62.158 γ = 83.31
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 MARMOSAIC 325 mm CCD 2009-11-23
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 33124
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3FK3 1.7 59 33124 33124 1730 96.57 0.16001 0.1578 0.1638 0.20193 0.2074 RANDOM 15.587
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] -0.65 0.9 -0.05 0.61 0.48 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.423 r_sphericity_free 20.537 r_dihedral_angle_4_deg 15.933 r_dihedral_angle_3_deg 12.704 r_scangle_it 8.513 r_dihedral_angle_1_deg 6.624 r_scbond_it 5.888 r_mcangle_it 4.495 r_rigid_bond_restr 3.653 r_sphericity_bonded 3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.423 r_sphericity_free 20.537 r_dihedral_angle_4_deg 15.933 r_dihedral_angle_3_deg 12.704 r_scangle_it 8.513 r_dihedral_angle_1_deg 6.624 r_scbond_it 5.888 r_mcangle_it 4.495 r_rigid_bond_restr 3.653 r_sphericity_bonded 3.59 r_mcbond_it 2.788 r_angle_refined_deg 1.51 r_mcbond_other 1.452 r_angle_other_deg 0.965 r_chiral_restr 0.117 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2440 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling