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Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 277 1.95 M ammonium sulfate and 0.1 M Na-acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 1.98 37.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.302 α = 90 b = 87.821 β = 107.44 c = 36.467 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 PILATUS3 2M 2015-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96600 ESRF MASSIF-1
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 1.2 43.91 96 0.06 0.072 0.041 0.997 9.4 2.9 48992
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 1.2 1.22 64.6 0.447 0.578 0.361 0.723 2
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 6HBA 1.2 30 46447 2513 95.94 0.1609 0.1591 0.169 0.1952 0.2022 RANDOM 15.226
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] -0.01 -0.22 0.32 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.772 r_sphericity_free 30.139 r_dihedral_angle_4_deg 17.211 r_dihedral_angle_3_deg 10.699 r_sphericity_bonded 10.275 r_dihedral_angle_1_deg 6.075 r_rigid_bond_restr 5.585 r_angle_refined_deg 2.132 r_angle_other_deg 0.975 r_chiral_restr 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.772 r_sphericity_free 30.139 r_dihedral_angle_4_deg 17.211 r_dihedral_angle_3_deg 10.699 r_sphericity_bonded 10.275 r_dihedral_angle_1_deg 6.075 r_rigid_bond_restr 5.585 r_angle_refined_deg 2.132 r_angle_other_deg 0.975 r_chiral_restr 0.165 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1404 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 35
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction