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Crystal structure of yeast Mmf1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JD1 PDB entry 1JD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.1 M Bis-Tris, 25% polyethylene glycol 3550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.618 α = 90 b = 77.618 β = 90 c = 43.911 γ = 120
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 RAYONIX MX-225 2009-12-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97012 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.74 50 99.3 0.104 0.104 14.8 11 9969 -3 29.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.8 94.5 0.25 0.25 7.2 7.8 929
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 PDB entry 1JD1 1.75 38.81 9481 483 99.34 0.18303 0.18114 0.1816 0.222 0.2244 RANDOM 22.841
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] -1.59 -0.79 -1.59 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_3_deg 14.037 r_dihedral_angle_4_deg 9.32 r_dihedral_angle_1_deg 4.873 r_scangle_it 4.284 r_scbond_it 2.603 r_mcangle_it 1.574 r_angle_refined_deg 1.139 r_mcbond_it 0.756 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_3_deg 14.037 r_dihedral_angle_4_deg 9.32 r_dihedral_angle_1_deg 4.873 r_scangle_it 4.284 r_scbond_it 2.603 r_mcangle_it 1.574 r_angle_refined_deg 1.139 r_mcbond_it 0.756 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 957 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling