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Crystal structure of yeast Urm1 at 1.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XO3 PDB ENTRY 1XO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 33-35% PEG 8000, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.97 37.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.871 α = 90 b = 62.681 β = 90 c = 27.244 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 4 2003-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
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 1.8 19.75 97.16 7848 7848 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 97.16
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 (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 ENTRY 1XO3 1.8 19.75 8474 7848 384 97.16 0.19175 0.19175 0.18837 0.2022 0.26295 0.2806 RANDOM 25.252
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.972 r_dihedral_angle_4_deg 12.421 r_scangle_it 11.876 r_dihedral_angle_3_deg 11.848 r_scbond_it 8.721 r_mcangle_it 6.84 r_mcbond_it 6.427 r_dihedral_angle_1_deg 5.527 r_mcbond_other 1.818 r_angle_refined_deg 1.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.972 r_dihedral_angle_4_deg 12.421 r_scangle_it 11.876 r_dihedral_angle_3_deg 11.848 r_scbond_it 8.721 r_mcangle_it 6.84 r_mcbond_it 6.427 r_dihedral_angle_1_deg 5.527 r_mcbond_other 1.818 r_angle_refined_deg 1.419 r_angle_other_deg 0.813 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.213 r_xyhbond_nbd_refined 0.198 r_symmetry_vdw_other 0.187 r_nbd_other 0.178 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.095 r_nbtor_other 0.078 r_xyhbond_nbd_other 0.042 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 801 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing