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Crystal structure of tRNA guanine-n1-methyltransferase from Bartonella henselae using MPCS.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MPCS 7 293 Initial crystal hit JCSG+ condition G7 15% PEG 3350, 0.1M succinic acid pH 7.0 optimized with microcapillary gradient, MPCS, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.017 α = 90 b = 84.467 β = 90 c = 97.192 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2009-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97946 SSRL BL7-1
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 2.5 50 99.9 0.116 18.2 8.9 16569
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) 2.5 2.59 100 0.492 3.8 8.5 1614
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 1p9p 2.5 50 16525 825 99.89 0.196 0.195 0.1938 0.225 0.2024 RANDOM 30.164
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] -0.99 -1.98 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.112 r_dihedral_angle_4_deg 18.305 r_dihedral_angle_3_deg 15.455 r_dihedral_angle_1_deg 6.039 r_scangle_it 3.296 r_scbond_it 1.999 r_mcangle_it 1.471 r_angle_refined_deg 1.381 r_mcbond_it 0.78 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.112 r_dihedral_angle_4_deg 18.305 r_dihedral_angle_3_deg 15.455 r_dihedral_angle_1_deg 6.039 r_scangle_it 3.296 r_scbond_it 1.999 r_mcangle_it 1.471 r_angle_refined_deg 1.381 r_mcbond_it 0.78 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3287 Nucleic Acid Atoms Solvent Atoms 93 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