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Crystal structure of Ugp1p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 6% PEG-4000, 15-18% glycerol, 140mM Mg-formate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.11 60.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.191 α = 90 b = 147.437 β = 90 c = 167.752 γ = 90
Symmetry Space Group I 2 2 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 MARMOSAIC 225 mm CCD 2004-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979350 ESRF ID23-1
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 3.1 110.978 98.9 0.102 0.102 3.9 4.2 24806
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 3.1 3.27 100 0.286 0.286 2.5 4.1 3645
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 (All) 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 1z90 3.1 19.99 24617 1261 98.29 0.23 0.226 0.2303 0.291 0.2906 RANDOM 74.44
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] 0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.572 r_dihedral_angle_4_deg 20.988 r_dihedral_angle_3_deg 20.743 r_dihedral_angle_1_deg 6.606 r_scangle_it 1.711 r_angle_refined_deg 1.444 r_scbond_it 1.01 r_mcangle_it 0.803 r_mcbond_it 0.461 r_symmetry_hbond_refined 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.572 r_dihedral_angle_4_deg 20.988 r_dihedral_angle_3_deg 20.743 r_dihedral_angle_1_deg 6.606 r_scangle_it 1.711 r_angle_refined_deg 1.444 r_scbond_it 1.01 r_mcangle_it 0.803 r_mcbond_it 0.461 r_symmetry_hbond_refined 0.366 r_nbtor_refined 0.312 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.22 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6607 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling