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Crystal structure of UTR4 protein (Unknown transcript 4 protein) (yel038w) from Saccharomyces cerevisiae at 2.28 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZS9 pdb entry 1zs9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 290 21.00% PEG 3350, 0.10M NP_Magnesium Nitrate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.6 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.688 α = 90 b = 102.016 β = 92.68 c = 77.227 γ = 90
Symmetry Space Group P 1 21 1
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 210 2004-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
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 2.28 61.54 99.9 0.088 0.088 4.5 3.6 52775 42.6
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 2.28 2.4 99.9 0.359 0.359 1.7 3.2
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 pdb entry 1zs9A 2.28 61.53 52503 2673 99.87 0.18 0.177 0.1845 0.229 0.2306 RANDOM 37.416
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] 1.67 -1 -1.76 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.321 r_dihedral_angle_4_deg 14.678 r_dihedral_angle_3_deg 9.746 r_scangle_it 6.423 r_scbond_it 4.84 r_dihedral_angle_1_deg 3.801 r_mcangle_it 2.754 r_mcbond_it 1.826 r_angle_refined_deg 1.604 r_angle_other_deg 1.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.321 r_dihedral_angle_4_deg 14.678 r_dihedral_angle_3_deg 9.746 r_scangle_it 6.423 r_scbond_it 4.84 r_dihedral_angle_1_deg 3.801 r_mcangle_it 2.754 r_mcbond_it 1.826 r_angle_refined_deg 1.604 r_angle_other_deg 1.196 r_mcbond_other 0.427 r_nbd_refined 0.173 r_nbtor_refined 0.155 r_symmetry_vdw_refined 0.142 r_symmetry_vdw_other 0.138 r_symmetry_hbond_refined 0.136 r_nbd_other 0.122 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.105 r_nbtor_other 0.071 r_metal_ion_refined 0.025 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6888 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing