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Nan Regulatory Protein Full-length from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TX9 isomerase domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293.15 15.5 mg/mL protein + 0.1 M phosphate/citrate, pH 4.2, 40% v/v PEG300 + 10 mM ligand (ManNac-6-P), cryoprotectant: 50:50 ethylene glycol/glycerol
Crystal Properties Matthews coefficient Solvent content 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.873 α = 90 b = 223.646 β = 90 c = 52.734 γ = 90
Symmetry Space Group C 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 EIGER X 16M 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.95 47.7 99.85 0.2461 0.994 7.49 8.9 15063 70.7
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 2.95 3.056 99.93 0.355 0.9 8.9
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 PDB entry 8TX9 2.95 47.7 1.34 15052 767 99.9 0.2539 0.2515 0.2604 0.3013 0.3205 72.93
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 5.1167 f_angle_d 0.6726 f_chiral_restr 0.0384 f_plane_restr 0.015 f_bond_d 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3712 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing