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Crystal structure of pHBMT1 from Populus trichocarpa
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 278 HEPES pH 7.6, Sodium sulfate decahydrate, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.007 α = 90 b = 53.153 β = 105.51 c = 103.43 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 278 PIXEL DECTRIS PILATUS 12M 2023-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.82 99.66 95.1 0.131 0.152 0.076 0.972 10 4.1 45448
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 2.2 99 0.175 0.204 0.103 0.424
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.82 99.66 42509 2251 93.25 0.17926 0.17738 0.188 0.21573 0.2234 RANDOM 15.402
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] -0.56 -1.13 0.72 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.436 r_long_range_B_refined 6.951 r_dihedral_angle_2_deg 6.926 r_long_range_B_other 6.841 r_dihedral_angle_1_deg 6.441 r_scangle_other 4.542 r_mcangle_it 3.335 r_mcangle_other 3.334 r_scbond_it 2.784 r_scbond_other 2.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.436 r_long_range_B_refined 6.951 r_dihedral_angle_2_deg 6.926 r_long_range_B_other 6.841 r_dihedral_angle_1_deg 6.441 r_scangle_other 4.542 r_mcangle_it 3.335 r_mcangle_other 3.334 r_scbond_it 2.784 r_scbond_other 2.784 r_mcbond_it 1.977 r_mcbond_other 1.977 r_angle_refined_deg 1.804 r_angle_other_deg 0.586 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3343 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHENIX phasing PDB_EXTRACT data extraction autoPROC data scaling