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The Bacillus pumilus chorismate mutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M MES pH 6.5
25% PEG 1500
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.898 α = 90 b = 94.864 β = 107.487 c = 77.305 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 PILATUS3 2M 2019-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.1 24.58 78.3 0.03 0.999 12.99 4.3 227592
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.139 22.6 0.9 0.244 0.65 3.1
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 3zo8 1.1 24.58 216961 1904 78.227 0.182 0.1823 0.1778 0.1965 0.193 17.981
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] -0.128 0.123 0.241 -0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.442 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 5.81 r_lrange_it 5.652 r_dihedral_angle_other_3_deg 5.383 r_lrange_other 5.257 r_scangle_it 3.701 r_scangle_other 3.701 r_scbond_other 2.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.442 r_dihedral_angle_4_deg 16.283 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 5.81 r_lrange_it 5.652 r_dihedral_angle_other_3_deg 5.383 r_lrange_other 5.257 r_scangle_it 3.701 r_scangle_other 3.701 r_scbond_other 2.282 r_scbond_it 2.278 r_angle_other_deg 1.939 r_mcangle_other 1.763 r_mcangle_it 1.76 r_angle_refined_deg 1.433 r_mcbond_other 1.153 r_mcbond_it 1.145 r_xyhbond_nbd_refined 0.276 r_nbd_other 0.246 r_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.196 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_other 0.149 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.076 r_bond_other_d 0.054 r_gen_planes_other 0.015 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5678 Nucleic Acid Atoms Solvent Atoms 820 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing