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Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to benzyl monophosphate and ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LNV CMA apo model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 0.1 M Bis-Tris pH 5.5
15% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.698 α = 90 b = 74.662 β = 90 c = 170.686 γ = 90
Symmetry Space Group P 21 21 21
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 Osmic Veri Max Mirror 2016-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 30 98.9 0.109 0.048 16.9 4.5 22277 28.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 89.5 0.412 0.221 0.874 2.89
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 CMA apo model 2.35 29.45 1.36 22223 1072 98.88 0.1894 0.1871 0.1876 0.234 0.2342 33.84
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 15.4195 f_angle_d 0.8565 f_chiral_restr 0.0454 f_plane_restr 0.0046 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3800 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing