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The Crystal Structure of BPGM from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 HM(P07738) 0.1M Hepes-NaOH pH 7.2, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.661 α = 90 b = 61.524 β = 95.32 c = 122.802 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 EIGER X 9M 2022-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953743 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 43.37 99.2 0.145 7.2 4 44995
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 97.6 0.754 2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 43.37 44995 2189 98.975 0.189 0.1872 0.1986 0.2293 0.238 25.064
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] -1.353 0.47 3.573 -2.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.396 r_dihedral_angle_4_deg 14.359 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 6.285 r_lrange_it 5.31 r_lrange_other 5.112 r_scangle_it 3.198 r_scangle_other 3.198 r_mcangle_it 2.526 r_mcangle_other 2.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.396 r_dihedral_angle_4_deg 14.359 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 6.285 r_lrange_it 5.31 r_lrange_other 5.112 r_scangle_it 3.198 r_scangle_other 3.198 r_mcangle_it 2.526 r_mcangle_other 2.525 r_scbond_it 1.921 r_scbond_other 1.92 r_mcbond_it 1.576 r_mcbond_other 1.575 r_angle_refined_deg 1.299 r_angle_other_deg 1.238 r_nbd_refined 0.199 r_nbd_other 0.187 r_symmetry_nbd_other 0.17 r_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.149 r_symmetry_xyhbond_nbd_other 0.099 r_ncsr_local_group_1 0.084 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4103 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing