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Structure of PopP2 in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1 Hepeps, pH7.5, 50 mM MgCl2, 30% PEG55OMME
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.36 α = 90 b = 89.36 β = 90 c = 79.871 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 210r 2020-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9774 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 50 100 0.984 15.9 9.2 15654
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 0.898
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 MOLECULAR REPLACEMENT FREE R-VALUE 5W3T 2.35185590332 35.4887640895 1.38062729577 15636 1562 99.82761923 0.196863902294 0.19293203813 0.2084 0.231361943868 0.2325 67.7970177276
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.382475487 f_angle_d 0.775254211399 f_chiral_restr 0.0275224075521 f_plane_restr 0.00387596262214 f_bond_d 0.00378195838651
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1853 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling Coot model building HKL-2000 data scaling PHASER phasing