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Crystal structure of a NIPSNAP domain protein from Burkholderia xenovorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 MORPHEUS G2: 10% w/v PEG8000, 20% v/v ethylene glycol, 100mM MES/imidazole pH 6.5, 20mM citrate, 20mM tartrate, 20mM acetate, 20mM oxamate, 20mM formate; dc; protein 9.94mg/mL; fsu3-9
Crystal Properties Matthews coefficient Solvent content 3.08 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.36 α = 90 b = 95.36 β = 90 c = 63.17 γ = 90
Symmetry Space Group I 4 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 CCD RAYONIX MX-225 2016-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.65 50 99.9 0.057 0.999 27.58 11.9 17813 -3 17.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 100 0.426 6.26
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 1VQS 1.65 35.346 1.36 17812 1831 99.93 0.1615 0.1586 0.1593 0.1873 0.1875 23.1097
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 17.671 f_angle_d 0.815 f_chiral_restr 0.047 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 808 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building XDS data reduction