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The Crystal Structure of BMX from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Imidazole pH6.5, 20% PEG 8000, 3% MPD
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.372 α = 90 b = 67.475 β = 90 c = 76.519 γ = 90
Symmetry Space Group P 21 21 21
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 2023-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953714 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 1.3 44.9 99.4 0.074 19.2 13.1 70778
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 1.3 1.33 0.979
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 1.3 44.899 70698 3494 99.366 0.129 0.1278 0.1238 0.1606 0.1557 18.648
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] 1.706 0.168 -1.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 48.358 r_dihedral_angle_2_deg 31.423 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 10.885 r_dihedral_angle_1_deg 6.339 r_lrange_it 4.3 r_lrange_other 3.87 r_scangle_it 2.67 r_scangle_other 2.67 r_scbond_it 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 48.358 r_dihedral_angle_2_deg 31.423 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 10.885 r_dihedral_angle_1_deg 6.339 r_lrange_it 4.3 r_lrange_other 3.87 r_scangle_it 2.67 r_scangle_other 2.67 r_scbond_it 2.326 r_scbond_other 2.325 r_rigid_bond_restr 2.319 r_mcangle_it 1.826 r_mcangle_other 1.826 r_angle_refined_deg 1.723 r_angle_other_deg 1.51 r_mcbond_other 1.344 r_mcbond_it 1.343 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.213 r_nbd_other 0.199 r_nbtor_refined 0.183 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2119 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing