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The crystal structure of EPD-BCP1 from a marine sponge
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, SITTING DROP 296 2-Amino-2-(hydroxymethyl)propane-1,3-diol, magnesium chloride, polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.749 α = 90 b = 101.38 β = 95.06 c = 112.588 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 S 6M 2022-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.44 75.32 99.9 0.104 0.125 0.068 0.981 7 3.3 61509 36.8
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 2.44 2.5 99.7 0.584 0.702 0.385 0.746 1.8 3.2
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 AlphaFold 2.44 75.32 61486 2954 99.891 0.204 0.2015 0.2097 0.2482 0.2558 43.642
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] 4.431 1.587 -2.54 -2.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.711 r_dihedral_angle_3_deg 14.773 r_lrange_it 8.97 r_lrange_other 8.97 r_dihedral_angle_1_deg 7.986 r_scangle_it 6.654 r_scangle_other 6.653 r_mcangle_it 6.636 r_mcangle_other 6.636 r_dihedral_angle_2_deg 5.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.711 r_dihedral_angle_3_deg 14.773 r_lrange_it 8.97 r_lrange_other 8.97 r_dihedral_angle_1_deg 7.986 r_scangle_it 6.654 r_scangle_other 6.653 r_mcangle_it 6.636 r_mcangle_other 6.636 r_dihedral_angle_2_deg 5.992 r_scbond_it 4.348 r_scbond_other 4.347 r_mcbond_it 4.311 r_mcbond_other 4.309 r_angle_refined_deg 1.403 r_angle_other_deg 0.489 r_xyhbond_nbd_refined 0.306 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.207 r_symmetry_nbd_other 0.196 r_nbd_other 0.194 r_nbtor_refined 0.171 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_refined 0.066 r_chiral_restr 0.064 r_ncsr_local_group_5 0.042 r_ncsr_local_group_7 0.042 r_ncsr_local_group_8 0.04 r_ncsr_local_group_6 0.039 r_ncsr_local_group_2 0.036 r_ncsr_local_group_3 0.036 r_ncsr_local_group_9 0.035 r_ncsr_local_group_12 0.035 r_ncsr_local_group_1 0.033 r_ncsr_local_group_10 0.031 r_ncsr_local_group_4 0.029 r_ncsr_local_group_11 0.022 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10660 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 687
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing