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The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Zn ions
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 10% PEG8000, MES pH 6.5, 0.2 M Zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.874 α = 90 b = 72.874 β = 90 c = 47.041 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.39 30 99.2 0.07 0.075 0.025 23.9 9.6 29388
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.44 98.4 0.337 0.356 0.113 0.964 9.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.39 23.87 27637 1485 99.14 0.1422 0.14172 0.1428 0.1514 0.151 RANDOM 14.247
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] 0.17 0.17 0.17 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_4_deg 18.077 r_dihedral_angle_3_deg 10.394 r_dihedral_angle_1_deg 7.872 r_long_range_B_refined 6.64 r_long_range_B_other 5.109 r_scangle_other 3.542 r_scbond_it 2.531 r_scbond_other 2.528 r_angle_refined_deg 2.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_4_deg 18.077 r_dihedral_angle_3_deg 10.394 r_dihedral_angle_1_deg 7.872 r_long_range_B_refined 6.64 r_long_range_B_other 5.109 r_scangle_other 3.542 r_scbond_it 2.531 r_scbond_other 2.528 r_angle_refined_deg 2.368 r_mcangle_other 1.674 r_mcangle_it 1.669 r_mcbond_it 1.18 r_mcbond_other 1.166 r_angle_other_deg 0.955 r_chiral_restr 0.143 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 958 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing