☰ Navigation Tabs
Crystal structure of MPXV P1 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.8 M Succinic acid, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.417 α = 90 b = 114.417 β = 90 c = 126.789 γ = 120
Symmetry Space Group P 3 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 100 PIXEL DECTRIS PILATUS 6M 2023-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979152 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.57 99.09 100 0.998 10.9 16 30914
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.71 0.74
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 THROUGHOUT 2I39 2.575 99 30763 1489 99.46 0.198 0.1961 0.2013 0.2418 0.2492 50.587
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] 0.752 0.376 0.752 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.408 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 16.255 r_lrange_other 11.998 r_lrange_it 11.994 r_scangle_it 10.009 r_scangle_other 10.008 r_mcangle_it 6.775 r_mcangle_other 6.775 r_scbond_it 6.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.408 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 16.255 r_lrange_other 11.998 r_lrange_it 11.994 r_scangle_it 10.009 r_scangle_other 10.008 r_mcangle_it 6.775 r_mcangle_other 6.775 r_scbond_it 6.604 r_scbond_other 6.603 r_dihedral_angle_1_deg 5.346 r_mcbond_it 4.712 r_mcbond_other 4.709 r_angle_refined_deg 1.597 r_angle_other_deg 1.371 r_nbd_other 0.233 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.188 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.163 r_ncsr_local_group_3 0.095 r_ncsr_local_group_13 0.091 r_ncsr_local_group_15 0.091 r_chiral_restr 0.088 r_ncsr_local_group_5 0.088 r_ncsr_local_group_10 0.088 r_ncsr_local_group_7 0.087 r_ncsr_local_group_12 0.085 r_ncsr_local_group_6 0.083 r_ncsr_local_group_8 0.081 r_ncsr_local_group_14 0.081 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_9 0.076 r_ncsr_local_group_1 0.072 r_ncsr_local_group_11 0.067 r_ncsr_local_group_4 0.064 r_ncsr_local_group_2 0.059 r_symmetry_xyhbond_nbd_refined 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5840 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing