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Streptococcus pneumoniae Phosphomevalonate Kinase in Complex with Phosphomevalonate and AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K49 PDB entry 1K49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 PEG 4000, MES, ethylene glycol, AMPPNP, phosphomevalonate, Mg, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.977 α = 90 b = 115.285 β = 90 c = 39.96 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 125 IMAGE PLATE RIGAKU RAXIS IV++ Osmic Blue 2004-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 23.4 91.3 0.045 4.1 23685 23685 10.5
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 1.97 81.4 0.145 5.6 1928
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1K49 1.9 23.38 23634 23634 1191 91.3 0.185 0.185 0.185 0.1849 0.207 0.2072 RANDOM 18.5
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] 2.86 -1.67 -1.19
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 3 c_scbond_it 2.07 c_mcangle_it 1.65 c_angle_deg 1.4 c_mcbond_it 1.15 c_improper_angle_d 0.77 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 46
Software Software Software Name Purpose CNS refinement CTR data collection DENZO data reduction SCALEPACK data scaling EPMR phasing