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Crystal structure of red chromoprotein from Olindias formosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG3350, sodium chloride, citrate, pH5.4
Crystal Properties Matthews coefficient Solvent content 4.7 77.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.476 α = 90 b = 116.476 β = 90 c = 161.444 γ = 90
Symmetry Space Group I 41 2 2
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 EIGER X 16M 2019-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.05 49.57 98.3 0.039 0.041 1 31.29 9.134 34497 48.789
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.17 95.2 0.54 0.571 0.917 3.65 9.19
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 (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 3gb3 2.05 49.57 32771 1725 98.27 0.1931 0.1922 0.2012 0.2109 0.2195 RANDOM 45.331
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] -0.73 -0.73 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.429 r_dihedral_angle_3_deg 15.371 r_dihedral_angle_4_deg 13.876 r_dihedral_angle_1_deg 7.727 r_angle_other_deg 2.465 r_angle_refined_deg 2.096 r_chiral_restr 0.095 r_bond_other_d 0.035 r_gen_planes_other 0.026 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.429 r_dihedral_angle_3_deg 15.371 r_dihedral_angle_4_deg 13.876 r_dihedral_angle_1_deg 7.727 r_angle_other_deg 2.465 r_angle_refined_deg 2.096 r_chiral_restr 0.095 r_bond_other_d 0.035 r_gen_planes_other 0.026 r_bond_refined_d 0.016 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1768 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing