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Crystal structure for Methylobacterium extorquens PqqC (truncation of natural CD 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. Drops suspended on siliconized glass. Protein solution: 8.0 mg/mL protein in buffer (50 mM Tris, pH 8.0, 200mM sodium chloride). Well solution: 100 mM HEPES, pH 8.07, 200 mM sodium chloride, and 23.75% w/v PEG-3350. All water used in well solution buffers was 0.55 mM sodium azide for fungal growth suppression. Protein:well solution was 1:1 (1 microL to 1 microL)
Crystal Properties Matthews coefficient Solvent content 2.04 39.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.501 α = 90 b = 114.185 β = 90 c = 145.403 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 PIXEL DECTRIS PILATUS3 6M 2015-07-18 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) 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 29.51 97.8 0.077 14.4 6.8 69169
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 29.51 65610 3492 97.84 0.19918 0.19719 0.2041 0.23634 0.2402 RANDOM 38.9
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] 1.11 0.26 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.457 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 17.105 r_dihedral_angle_1_deg 6.811 r_long_range_B_refined 4.844 r_long_range_B_other 4.838 r_scangle_other 3.606 r_mcangle_it 2.829 r_mcangle_other 2.829 r_angle_refined_deg 2.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.457 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 17.105 r_dihedral_angle_1_deg 6.811 r_long_range_B_refined 4.844 r_long_range_B_other 4.838 r_scangle_other 3.606 r_mcangle_it 2.829 r_mcangle_other 2.829 r_angle_refined_deg 2.457 r_scbond_it 2.409 r_scbond_other 2.409 r_mcbond_it 1.978 r_mcbond_other 1.978 r_angle_other_deg 1.448 r_chiral_restr 0.241 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6964 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHASER phasing XDS data reduction