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Crystal Structure of the methyltransferase Slr1183 from Synechocystis sp. PCC 6803, Northeast Structural Genomics Consortium Target SgR145
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I6G 2i6g and 2kw5 experimental model PDB 2KW5 2i6g and 2kw5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch, under oil 4 277 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Sodium Malonate (pH 4.0) and 12% PEG 3350. , Microbatch, under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.44 α = 115.49 b = 53.792 β = 95.66 c = 53.845 γ = 84.35
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 4 mirrors 2008-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 1.00684 NSLS X4A
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 2.2 30 98.1 0.046 0.037 23.4 3.2 21262 20859 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 96.3 0.227 0.163 4.7 3.1 2113
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2i6g and 2kw5 2.2 19.61 2 2 21144 17804 863 84.2 0.228 0.226 0.224 0.2393 0.249 0.2615 RANDOM 42.6
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] -4.85 -0.71 -2.11 -5.7 14.18 10.55
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.5 c_angle_deg 1.3 c_improper_angle_d 0.93 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2656 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement