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Apo form of a putative sugar kinase MK0840 from Methanopyrus kandleri (orthorhombic space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BG8 PDB ENTRY 4BG8 CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 293 0.5 M POTASSIUM THIOCYANATE, 0.1 M SODIUM ACETATE PH 4.6 AT 293 K
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.043 α = 90 b = 115.967 β = 90 c = 48.363 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD 2010-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 61.8 99.5 0.09 14.6 4.6 33085 2 21.31
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 1.9 2.02 97.5 0.71 2.17 4.6
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 4BG8 CHAIN A 1.902 61.805 1.17 33085 3100 99.28 0.1802 0.1787 0.1828 0.2084 0.211 28.6
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] 5.3344 -3.7407 -1.5937
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.08 f_angle_d 1.375 f_chiral_restr 0.076 f_bond_d 0.013 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2391 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing