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Crystal Structure of CalO4 from Micromonospora echinospora
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 6.5 293 0.12 M MES, 1.2 M magnesium sulfate heptahydrate
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.696 α = 90 b = 95.635 β = 95.63 c = 172.584 γ = 90
Symmetry Space Group I 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 110 PIXEL DECTRIS EIGER X 16M 2025-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.919689 NSLS-II 17-ID-1
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 1.64 29.24 99.9 0.04786 0.06768 0.04786 0.997 7.36 3.5 94115
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 1.64 1.699 0.705
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 1.64 29.24 94114 4745 99.908 0.164 0.163 0.1618 0.1928 0.1905 17.2
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] -0.004 -0.003 0.57 -0.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.671 r_dihedral_angle_3_deg 12.229 r_dihedral_angle_2_deg 6.548 r_dihedral_angle_1_deg 6.153 r_lrange_it 5.69 r_scangle_it 4.431 r_scbond_it 3.079 r_mcangle_it 2.697 r_angle_refined_deg 2.155 r_mcbond_it 1.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.671 r_dihedral_angle_3_deg 12.229 r_dihedral_angle_2_deg 6.548 r_dihedral_angle_1_deg 6.153 r_lrange_it 5.69 r_scangle_it 4.431 r_scbond_it 3.079 r_mcangle_it 2.697 r_angle_refined_deg 2.155 r_mcbond_it 1.933 r_nbtor_refined 0.32 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.208 r_chiral_restr 0.167 r_xyhbond_nbd_refined 0.145 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4994 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing