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SpAga wild type apo structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 0.1 M sodium acetate:acetic acid, 1.1 M ammonium tartrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.61 52.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.724 α = 90 b = 127.241 β = 90 c = 151.82 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 PIXEL DECTRIS PILATUS 200K 2018-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.5419
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 30 99.2 0.152 0.077 0.986 9 4.7 44566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 98.1 0.406 0.244 0.805 2.1 3.7
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 (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 4FNU 2.2 29.68 41959 2298 98.28 0.1846 0.1819 0.1818 0.2334 0.2333 RANDOM 34.826
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 0.08 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.688 r_dihedral_angle_4_deg 15.489 r_dihedral_angle_3_deg 13.682 r_dihedral_angle_1_deg 7.431 r_angle_refined_deg 1.338 r_chiral_restr 0.105 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5749 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction