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Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 298 PEG3350, Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.441 α = 90 b = 164.441 β = 90 c = 95.044 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS3 6M MIRROR 2015-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000010 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 2.66 116.28 99.6 0.322 0.33 0.329 0.049 0.998 17.3 44 37790 54.44
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 2.66 2.68 99.4 2.089 2.4 31.2
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 5LC9 2.66 116.28 37723 1840 99.4 0.21 0.208 0.2178 0.253 0.25 RANDOM 46.39
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] -5.8826 -5.8826 11.7652
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.38 t_omega_torsion 2.57 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.38 t_omega_torsion 2.57 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8620 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 163
Software Software Software Name Purpose Aimless data scaling MOLREP phasing BUSTER-TNT refinement PDB_EXTRACT data extraction autoPROC data reduction