☰ Navigation Tabs
X-ray structure of the adduct formed by dirhodium tetraacetate with a C-phycocyanin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1-0.2 M magnesium chloride
0.1 M hepes buffer pH 6.5
9-10% PEG4k
Crystal Properties Matthews coefficient Solvent content 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.586 α = 90 b = 188.5 β = 90 c = 207.212 γ = 90
Symmetry Space Group P 2 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 PILATUS 6M-F 2020-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.169 188.5 94.2 0.34 0.1 0.996 6.6 12.9 102759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.31 63.6 2.13 0.656 0.564 11.6
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 2.169 139.827 102759 5000 81.157 0.228 0.2267 0.2299 0.2633 0.2684 35.727
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] 0.71 -0.398 -0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.394 r_dihedral_angle_4_deg 16.315 r_dihedral_angle_3_deg 15.378 r_lrange_other 6.751 r_lrange_it 6.733 r_dihedral_angle_1_deg 5.356 r_scangle_other 5.283 r_scangle_it 5.255 r_mcangle_it 4.405 r_mcangle_other 4.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.394 r_dihedral_angle_4_deg 16.315 r_dihedral_angle_3_deg 15.378 r_lrange_other 6.751 r_lrange_it 6.733 r_dihedral_angle_1_deg 5.356 r_scangle_other 5.283 r_scangle_it 5.255 r_mcangle_it 4.405 r_mcangle_other 4.404 r_scbond_it 3.452 r_scbond_other 3.405 r_mcbond_it 3.004 r_mcbond_other 3.004 r_angle_refined_deg 1.729 r_angle_other_deg 1.32 r_nbd_other 0.253 r_nbd_refined 0.223 r_ext_dist_refined_d 0.211 r_symmetry_nbd_other 0.192 r_xyhbond_nbd_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.157 r_symmetry_nbd_refined 0.116 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.066 r_ncsr_local_group_33 0.063 r_ncsr_local_group_10 0.062 r_ncsr_local_group_42 0.062 r_ncsr_local_group_45 0.061 r_symmetry_xyhbond_nbd_other 0.06 r_ncsr_local_group_19 0.06 r_ncsr_local_group_23 0.06 r_ncsr_local_group_40 0.06 r_ncsr_local_group_44 0.06 r_ncsr_local_group_1 0.057 r_ncsr_local_group_18 0.057 r_ncsr_local_group_5 0.055 r_ncsr_local_group_30 0.055 r_ncsr_local_group_43 0.055 r_ncsr_local_group_27 0.054 r_ncsr_local_group_16 0.053 r_ncsr_local_group_15 0.051 r_ncsr_local_group_17 0.051 r_ncsr_local_group_38 0.051 r_ncsr_local_group_7 0.05 r_ncsr_local_group_36 0.05 r_ncsr_local_group_21 0.048 r_ncsr_local_group_2 0.047 r_ncsr_local_group_8 0.047 r_ncsr_local_group_29 0.047 r_ncsr_local_group_9 0.046 r_ncsr_local_group_13 0.046 r_ncsr_local_group_4 0.045 r_ncsr_local_group_41 0.045 r_ncsr_local_group_3 0.044 r_ncsr_local_group_6 0.044 r_ncsr_local_group_22 0.044 r_ncsr_local_group_28 0.044 r_ncsr_local_group_32 0.043 r_ncsr_local_group_25 0.042 r_ncsr_local_group_35 0.042 r_ncsr_local_group_12 0.041 r_ncsr_local_group_14 0.039 r_ncsr_local_group_31 0.039 r_ncsr_local_group_24 0.037 r_ncsr_local_group_34 0.036 r_ncsr_local_group_20 0.035 r_ncsr_local_group_26 0.035 r_ncsr_local_group_37 0.034 r_ncsr_local_group_11 0.026 r_ncsr_local_group_39 0.023 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14826 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 947
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling REFMAC phasing