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C4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 294.15 0.1 M MOPS (pH 7.0), 0.1 M magnesium formiate, 17 % (w/v) PEG 3350, 10 mM phosphoenol pyruvate, 0.75 mM 2'-Br-dAppNHp
Crystal Properties Matthews coefficient Solvent content 3.1 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.98 α = 106.22 b = 108.45 β = 101.81 c = 152.76 γ = 98.32
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 ADSC QUANTUM 315r 2014-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.919344 ESRF BM30A
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 2.9 20 98.8 0.097 0.995 12.4 3.9 90103 -3 37.38
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 2.9 3 98.7 0.445 2.9 3.9
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 5JVJ 2.9 19.79 90103 1875 98.27 0.2119 0.2115 0.2118 0.2315 0.2338 RANDOM 46.8852
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] -4.86 -0.25 -0.15 1.29 0.15 2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 13.824 r_dihedral_angle_1_deg 5.299 r_angle_other_deg 3.672 r_angle_refined_deg 1.507 r_mcangle_it 0.955 r_mcbond_it 0.525 r_mcbond_other 0.525 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 13.824 r_dihedral_angle_1_deg 5.299 r_angle_other_deg 3.672 r_angle_refined_deg 1.507 r_mcangle_it 0.955 r_mcbond_it 0.525 r_mcbond_other 0.525 r_chiral_restr 0.081 r_bond_refined_d 0.017 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23494 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 140
Software Software Software Name Purpose XDS data scaling XDS data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction