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Crystal structure of tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 289 21.0 mg/mL protein, expression tag not cleaved prior to crystallization; 0.1 M Na citrate pH 4.0, 8% PEG 3350, 10% glycerol, crystal tracking ID 205756f1 and q1x5b1-7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.291 α = 90 b = 104.304 β = 90 c = 99.105 γ = 90
Symmetry Space Group P 21 21 2
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 315 2009-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.25 50 100 0.064 30.95 7.2 52092
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 2.25 2.33 99.9 0.584 3.4 6.9 5115
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 3IEF 2.25 50 51937 2645 99.66 0.205 0.203 0.1975 0.234 0.2279 RANDOM 25.526
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] 0.65 0.22 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.335 r_dihedral_angle_4_deg 15.763 r_dihedral_angle_3_deg 14.533 r_dihedral_angle_1_deg 5.091 r_scangle_it 3.484 r_scbond_it 2.174 r_mcangle_it 1.541 r_angle_refined_deg 1.295 r_mcbond_it 0.83 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.335 r_dihedral_angle_4_deg 15.763 r_dihedral_angle_3_deg 14.533 r_dihedral_angle_1_deg 5.091 r_scangle_it 3.484 r_scbond_it 2.174 r_mcangle_it 1.541 r_angle_refined_deg 1.295 r_mcbond_it 0.83 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6003 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling