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Crystal structure of redox-inhibited phosphoribulokinase from Synechococcus sp. (strain PCC 6301)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HZL preliminary version of 6HZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 20 % PEG-3350, 200 mM ammonium fluoride
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.825 α = 90 b = 140.825 β = 90 c = 205.708 γ = 120
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 6M 2017-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.03320 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 49.12 99.9 0.073 0.081 0.034 0.999 12 5.6 30873 62.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 1.418 1.561 0.646 0.595 5.8
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 preliminary version of 6HZL 2.4 30 29347 1503 99.82 0.2242 0.2225 0.2225 0.2569 0.255 RANDOM 99.671
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] 0.38 0.19 0.38 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_3_deg 15.283 r_dihedral_angle_1_deg 5.586 r_angle_refined_deg 1.218 r_angle_other_deg 0.789 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.504 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_3_deg 15.283 r_dihedral_angle_1_deg 5.586 r_angle_refined_deg 1.218 r_angle_other_deg 0.789 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4954 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction