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Structure of human PYCR1 complexed with L-tetrahydro-2-furoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Crystallization reservoir contained 3 M NaCl and 0.1 M HEPES at pH 7.5-8.0. Crystal was soaked in cryobuffer containing 50 mM L-tetrahydro-2-furoic acid and 30% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.028 α = 90 b = 120.17 β = 108.92 c = 87.868 γ = 90
Symmetry Space Group C 1 2 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 CMOS RDI CMOS_8M 2015-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.35 60.085 96.3 0.082 0.096 0.051 0.997 13.2 3.5 72417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.4 75.2 0.579 0.694 0.379 0.716 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5UAX 2.35 60.085 1.89 72279 3593 96.04 0.1792 0.1768 0.1801 0.2237 0.225 46.4378
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9814 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 41
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing