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Crystal structure for Methylobacterium extorquens PqqCD (natural fusion)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 500 microL well volumes. Protein solution: 8.0 mg/mL protein, 50 mM Tris, pH 7.9, 100 mM sodium chloride, and 1 mM TCEP. Well solution: 100 mM HEPES, pH 6.7, 19% w/v PEG-4000, 10% isopropanol. Water used in the well solutions contained 0.55 mM sodium azide. Hanging drops were 1 microL protein solution and 1 microL well solution
Crystal Properties Matthews coefficient Solvent content 2.9 57.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.936 α = 90 b = 103.936 β = 90 c = 243.485 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS3 6M 2015-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.85 243.49 98.5 0.062 0.032 17 4.5 31557
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 1otv 2.85 243.49 29899 1593 98.38 0.2569 0.25314 0.255 0.32707 0.328 RANDOM
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] 1.09 1.09 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.886 r_dihedral_angle_3_deg 21.46 r_dihedral_angle_4_deg 18.939 r_long_range_B_refined 8.509 r_long_range_B_other 8.503 r_dihedral_angle_1_deg 8.119 r_mcangle_other 5.641 r_mcangle_it 5.64 r_scangle_other 5.496 r_mcbond_it 3.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.886 r_dihedral_angle_3_deg 21.46 r_dihedral_angle_4_deg 18.939 r_long_range_B_refined 8.509 r_long_range_B_other 8.503 r_dihedral_angle_1_deg 8.119 r_mcangle_other 5.641 r_mcangle_it 5.64 r_scangle_other 5.496 r_mcbond_it 3.615 r_mcbond_other 3.613 r_scbond_it 3.444 r_scbond_other 3.444 r_angle_refined_deg 2.088 r_angle_other_deg 1.241 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6570 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHASER phasing XDS data reduction