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Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329 -388), fused to MBP. Space group P212121
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 6.7 291.15 20%(w/v) PEG 5000 mono-methyl ether, 0.2 M Pipes/KOH pH 6.7, 0.1M Proline, Crystals were transferred into the following cryo-protective solution before vitrification: 20%(w/v) PEG 5000 mono-methyl ether, 0.2 M Pipes/KOH pH 6.7, 0.1M Proline, 5mM Maltose, 20%(v/v) Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.617 α = 90 b = 77.421 β = 90 c = 79.132 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 110 IMAGE PLATE MAR scanner 345 mm plate 2016-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.54 31.3 97.4 0.024 0.026 0.01 44.63 6.8 59991 17.356
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 1.54 1.57 66.5 0.186 0.204 0.081 0.982 5.6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4kyc 1.551 31.24 59927 3092 98.491 0.165 0.1637 0.1637 0.1887 0.1886 16.956
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] -0.445 0.56 -0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.969 r_dihedral_angle_4_deg 14.15 r_dihedral_angle_3_deg 13.217 r_dihedral_angle_1_deg 5.664 r_lrange_it 4.658 r_scangle_it 3.114 r_scbond_it 2.098 r_mcangle_it 1.605 r_angle_refined_deg 1.529 r_mcbond_it 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.969 r_dihedral_angle_4_deg 14.15 r_dihedral_angle_3_deg 13.217 r_dihedral_angle_1_deg 5.664 r_lrange_it 4.658 r_scangle_it 3.114 r_scbond_it 2.098 r_mcangle_it 1.605 r_angle_refined_deg 1.529 r_mcbond_it 1.06 r_nbtor_refined 0.316 r_symmetry_nbd_refined 0.24 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.208 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.1 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3297 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing Coot model building