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Bacillus phage VMY22 p56 in complex with Bacillus weidmannii Ung
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.2 M Sodium iodide, 0.1M Bis-tris propane pH 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.327 α = 90 b = 97.495 β = 111.362 c = 100.555 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 289.15 PIXEL DECTRIS EIGER2 XE 16M 2017-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9762 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.45 48.87 99.8 0.993 2.53 4.4 56337
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.52 0.821
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 4L5N 2.45 48.87 56318 2745 99.674 0.206 0.2044 0.2048 0.237 0.2376 34.39
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] 0.146 -0.308 1.136 -0.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.749 r_dihedral_angle_4_deg 20.77 r_dihedral_angle_3_deg 15.121 r_dihedral_angle_1_deg 6.505 r_lrange_it 5.985 r_lrange_other 5.984 r_scangle_it 4.458 r_scangle_other 4.457 r_mcangle_it 3.676 r_mcangle_other 3.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.749 r_dihedral_angle_4_deg 20.77 r_dihedral_angle_3_deg 15.121 r_dihedral_angle_1_deg 6.505 r_lrange_it 5.985 r_lrange_other 5.984 r_scangle_it 4.458 r_scangle_other 4.457 r_mcangle_it 3.676 r_mcangle_other 3.676 r_scbond_it 2.828 r_scbond_other 2.826 r_mcbond_it 2.396 r_mcbond_other 2.396 r_angle_refined_deg 1.413 r_angle_other_deg 1.189 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_other 0.199 r_nbd_refined 0.197 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.14 r_ncsr_local_group_9 0.128 r_ncsr_local_group_15 0.125 r_ncsr_local_group_14 0.122 r_symmetry_nbd_refined 0.121 r_ncsr_local_group_10 0.119 r_ncsr_local_group_8 0.118 r_ncsr_local_group_16 0.117 r_ncsr_local_group_17 0.117 r_ncsr_local_group_13 0.114 r_ncsr_local_group_19 0.112 r_ncsr_local_group_30 0.112 r_ncsr_local_group_23 0.109 r_ncsr_local_group_27 0.106 r_ncsr_local_group_32 0.106 r_ncsr_local_group_11 0.104 r_ncsr_local_group_22 0.102 r_ncsr_local_group_34 0.1 r_ncsr_local_group_21 0.095 r_ncsr_local_group_18 0.093 r_ncsr_local_group_20 0.093 r_ncsr_local_group_12 0.088 r_ncsr_local_group_24 0.085 r_ncsr_local_group_7 0.084 r_ncsr_local_group_6 0.08 r_ncsr_local_group_1 0.076 r_ncsr_local_group_5 0.075 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.073 r_ncsr_local_group_2 0.073 r_ncsr_local_group_4 0.071 r_chiral_restr 0.065 r_ncsr_local_group_33 0.063 r_ncsr_local_group_29 0.061 r_ncsr_local_group_3 0.058 r_ncsr_local_group_26 0.056 r_ncsr_local_group_25 0.055 r_ncsr_local_group_31 0.049 r_ncsr_local_group_28 0.024 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 10913 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing