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Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329 -388), fused to MBP. Space group P21.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 1.65 M Ammonium sulphate, 0.2M Malic acid/KOH pH 5.5, Crystals were transferred into the following cryo-protective solution before vitrification: 1.65 M Ammonium sulphate, 0.2M Malic acid/KOH pH 5.5, 5mM Maltose, 1 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.38 48.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.561 α = 90 b = 70.074 β = 96.472 c = 111.739 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 CCD ADSC QUANTUM 210 2016-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.31 59.33 70.7 0.051 0.061 0.032 10.9 3.2 149703 12.824
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.31 1.33 2.9 0.607 0.857 0.605 0.783 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4kyc 1.312 59.329 149527 7389 71.002 0.152 0.1498 0.1427 0.1957 0.1903 Random Selection 13.824
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] -0.787 -0.763 -0.354 1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.487 r_sphericity_free 24.246 r_dihedral_angle_4_deg 16.625 r_dihedral_angle_3_deg 12.58 r_sphericity_bonded 10.995 r_dihedral_angle_1_deg 5.47 r_lrange_it 3.196 r_scangle_it 2.277 r_scbond_it 1.863 r_rigid_bond_restr 1.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.487 r_sphericity_free 24.246 r_dihedral_angle_4_deg 16.625 r_dihedral_angle_3_deg 12.58 r_sphericity_bonded 10.995 r_dihedral_angle_1_deg 5.47 r_lrange_it 3.196 r_scangle_it 2.277 r_scbond_it 1.863 r_rigid_bond_restr 1.737 r_mcangle_it 1.488 r_angle_refined_deg 1.454 r_mcbond_it 1.139 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.237 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.182 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.098 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6636 Nucleic Acid Atoms Solvent Atoms 1321 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing Coot model building