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Crystal structure of VAO-type flavoprotein MtVAO713 from Myceliophthora thermophila C1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other MtVAO615
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 25% PEG3350, 0.1 M Tris pH 8.5-9.0
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.195 α = 90 b = 108.506 β = 90 c = 135.989 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2015-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.574
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.2 54.3 98.8 0.148 0.114 0.968 3.9 2.1 120921
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 97.3 0.483 0.479 0.532 1.6 2.1
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 MtVAO615 2.2 54.25 114990 5894 98.58 0.19793 0.19585 0.1995 0.23859 0.2405 RANDOM 19.44
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] -5.14 4.8 23.4 -18.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.307 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 13.429 r_dihedral_angle_1_deg 6.14 r_long_range_B_refined 3.571 r_long_range_B_other 3.469 r_angle_refined_deg 1.575 r_angle_other_deg 1.009 r_scangle_other 0.544 r_scbond_it 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.307 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 13.429 r_dihedral_angle_1_deg 6.14 r_long_range_B_refined 3.571 r_long_range_B_other 3.469 r_angle_refined_deg 1.575 r_angle_other_deg 1.009 r_scangle_other 0.544 r_scbond_it 0.325 r_scbond_other 0.325 r_chiral_restr 0.087 r_mcangle_it 0.078 r_mcangle_other 0.078 r_mcbond_it 0.042 r_mcbond_other 0.042 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 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 17597 Nucleic Acid Atoms Solvent Atoms 1522 Heterogen Atoms 428
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing