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Apo structure of TP domain from Haemophilus influenzae Penicillin-Binding Protein 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20% PEG 3,350 and 0.2 M KNO3
Crystal Properties Matthews coefficient Solvent content 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.014 α = 90 b = 93.632 β = 95.46 c = 95.83 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 PIXEL DECTRIS PILATUS 6M 2018-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.44 95.4 91.8 0.086 12.6 4.4 33806
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.69
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4BJP 2.44 95.4 33799 67.78 0.22374 0.22374 0.2289 62.372
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] 0.29 -0.09 0.22 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.247 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_3_deg 14.758 r_long_range_B_refined 13.04 r_long_range_B_other 13.039 r_scangle_other 9.427 r_mcangle_it 8.177 r_mcangle_other 8.177 r_dihedral_angle_1_deg 7.355 r_scbond_it 5.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.247 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_3_deg 14.758 r_long_range_B_refined 13.04 r_long_range_B_other 13.039 r_scangle_other 9.427 r_mcangle_it 8.177 r_mcangle_other 8.177 r_dihedral_angle_1_deg 7.355 r_scbond_it 5.886 r_scbond_other 5.885 r_mcbond_it 5.239 r_mcbond_other 5.239 r_angle_refined_deg 1.658 r_angle_other_deg 1.192 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 8705 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction autoPROC data scaling MrBUMP phasing