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Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942), thiol-oxidized form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 277 25.5% PEG-3350 and 0.1 M Na-acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.896 α = 90 b = 89.185 β = 107.7 c = 36.29 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 2M 2015-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 1.65 44.59 99.2 0.086 0.099 0.047 0.995 9.4 4.2 19621
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 1.65 1.67 88.5 0.833 0.963 0.473 0.548 3.8
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 6HAS 1.65 30 18569 974 99.73 0.2006 0.1985 0.2068 0.2413 0.2472 RANDOM 27.824
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] -0.35 -0.06 -0.15 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.859 r_dihedral_angle_4_deg 25.358 r_dihedral_angle_3_deg 14.043 r_dihedral_angle_1_deg 6.908 r_angle_refined_deg 1.832 r_angle_other_deg 1.312 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.859 r_dihedral_angle_4_deg 25.358 r_dihedral_angle_3_deg 14.043 r_dihedral_angle_1_deg 6.908 r_angle_refined_deg 1.832 r_angle_other_deg 1.312 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1403 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction