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Crystal structure of a chitinase-modifying protein from Fusarium vanettenii (Fvan-cmp)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model RoseTTAFold RoseTTAFold prediction
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 287 NaCl, MES, PEG 4000. Cryoprotected with additional 10% PEG 400.
Crystal Properties Matthews coefficient Solvent content 3.09 60.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.795 α = 90 b = 94.651 β = 90 c = 110.478 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 93 IMAGE PLATE RIGAKU RAXIS IV++ 2019-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54
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 2.19 100 99.1 0.356 0.389 0.153 5.4 6.1 43664
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 2.2 2.24 99.2 1.202 1.316 0.523 0.567 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT RoseTTAFold prediction 2.194 53.76 43607 2197 98.92 0.2 0.1971 0.1971 0.2532 0.2531 RANDOM 33.291
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] -0.004 0.064 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.462 r_dihedral_angle_4_deg 15.882 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 7.158 r_lrange_it 5.794 r_lrange_other 5.726 r_scangle_it 4.429 r_scangle_other 4.429 r_mcangle_other 3.4 r_mcangle_it 3.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.462 r_dihedral_angle_4_deg 15.882 r_dihedral_angle_3_deg 13.523 r_dihedral_angle_1_deg 7.158 r_lrange_it 5.794 r_lrange_other 5.726 r_scangle_it 4.429 r_scangle_other 4.429 r_mcangle_other 3.4 r_mcangle_it 3.399 r_scbond_it 2.779 r_scbond_other 2.778 r_mcbond_it 2.302 r_mcbond_other 2.302 r_angle_refined_deg 1.475 r_angle_other_deg 1.284 r_nbd_other 0.206 r_symmetry_nbd_refined 0.194 r_nbd_refined 0.188 r_symmetry_nbd_other 0.173 r_symmetry_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.165 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4723 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing