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SH3-like domain from Penicillium virgatum muramidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PACT C9=0.2 M LiCl, 0.1 M Hepes pH 7.0, 20% PEG 6K, MMS (microseed matrix screening) from JCSG, C7=0.2 M zinc acetate dehydrate, 0.1 M sodium acetate, 10%w/v PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.142 α = 90 b = 59.824 β = 112.131 c = 36.109 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 100 CCD ADSC QUANTUM 315 2017-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.28249 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 59.82 93.8 0.082 0.108 0.069 0.995 7.4 4 21381
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 1.5 1.53 66.8 0.967 1.282 0.835 0.261 1 3.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8B2S 1.5 33.479 21359 1052 93.218 0.164 0.1631 0.1725 0.1897 16.849
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] -3.759 2.023 3.359 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.335 r_dihedral_angle_3_deg 9.558 r_dihedral_angle_1_deg 6.603 r_lrange_it 4.768 r_lrange_other 4.707 r_scangle_it 3.895 r_scangle_other 3.893 r_mcangle_other 2.885 r_mcangle_it 2.867 r_scbond_it 2.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.335 r_dihedral_angle_3_deg 9.558 r_dihedral_angle_1_deg 6.603 r_lrange_it 4.768 r_lrange_other 4.707 r_scangle_it 3.895 r_scangle_other 3.893 r_mcangle_other 2.885 r_mcangle_it 2.867 r_scbond_it 2.735 r_scbond_other 2.733 r_mcbond_other 1.998 r_mcbond_it 1.997 r_angle_refined_deg 1.795 r_dihedral_angle_2_deg 1.717 r_angle_other_deg 0.565 r_nbd_refined 0.212 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.176 r_nbd_other 0.118 r_xyhbond_nbd_refined 0.103 r_ncsr_local_group_1 0.093 r_metal_ion_refined 0.085 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.082 r_symmetry_nbd_refined 0.031 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1085 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 17
Software Software Software Name Purpose XDS data reduction xia2 data reduction Aimless data scaling MOLREP phasing REFMAC refinement