☰ Navigation Tabs
Crystal structure of a putative uridine phosphorylase from Actinobacillus succinogenes 130Z (Target NYSGRC-029667 )
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG1 #81: 0.2 M sodium formate, 20% (w/v) PEG 3350); Cryoprotection (33% glycerol), Vapor Diffusion, Sitting Drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.422 α = 90 b = 120.595 β = 90 c = 176.879 γ = 90
Symmetry Space Group P 21 21 21
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 MX225HE MIRRORS 2013-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979310 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 99.9 0.2 13.18 14.6 126139 30.7
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 2 2.03 98.8 1.23 12.5 6175
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 30 125108 6187 99.88 0.1713 0.1694 0.1702 0.2081 0.209 RANDOM 33.385
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] 0.63 0.64 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 14.74 r_dihedral_angle_3_deg 13.467 r_dihedral_angle_1_deg 5.908 r_mcangle_it 2.553 r_mcbond_it 1.619 r_mcbond_other 1.618 r_angle_refined_deg 1.344 r_angle_other_deg 0.766 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 14.74 r_dihedral_angle_3_deg 13.467 r_dihedral_angle_1_deg 5.908 r_mcangle_it 2.553 r_mcbond_it 1.619 r_mcbond_other 1.618 r_angle_refined_deg 1.344 r_angle_other_deg 0.766 r_chiral_restr 0.074 r_bond_refined_d 0.008 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 11431 Nucleic Acid Atoms Solvent Atoms 803 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction SCALEPACK data scaling SHELX phasing SHELXD phasing SHELXE model building