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Crystal structure of Rhodospirillum rubrum Rru_A0973
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1 - 2 ul protein mixed with 1 ul well solution over 1 ml well solution.
0.14 M calcium acetate
15 % (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 3.17 61.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.184 α = 90 b = 120.533 β = 95.36 c = 140.25 γ = 90
Symmetry Space Group P 1 21 1
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 2015-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.7311 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.064 49.63 99.2 0.123 0.147 10.6 6.4 395746 395746
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 2.064 2.1 88.6 0.79 1.6 4.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3K6C 2.064 49.627 1.34 385749 19192 97.96 0.173 0.1712 0.1674 0.2061 0.2028 Random Selection
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 13.768 f_angle_d 1.264 f_chiral_restr 0.055 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22233 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms 138
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing