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Crystal Structure of OrfX in Complex with S-Adenosylmethionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VH0 PDB ENTRY 1VH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 20% PEG 550 MME, 5 mM ZnSO4, 0.1M Na 2-(N-morpholino) ethanesulfonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.8 α = 90 b = 84.29 β = 90 c = 55.73 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2010-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.7 28.6 95.8 0.059 19.5 8.4 19664 20528 26
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 1.7 1.76 93.8 0.347 5.4 1862
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1VH0 1.7 26.43 19664 19662 1008 95.6 0.214 0.207 0.207 0.2065 0.247 0.2469 RANDOM 30.8
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] -2.15 5.35 -3.2
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 6.93 c_scbond_it 5.16 c_mcangle_it 3.87 c_mcbond_it 3.18 c_angle_deg 1.7 c_improper_angle_d 1.21 c_bond_d 0.018 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 6.93 c_scbond_it 5.16 c_mcangle_it 3.87 c_mcbond_it 3.18 c_angle_deg 1.7 c_improper_angle_d 1.21 c_bond_d 0.018 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1314 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 45
Software Software Software Name Purpose CrystalClear data collection PHASER phasing CNS refinement CrystalClear data reduction CrystalClear data scaling