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Y201W mutant of the orange carotenoid protein from Synechocystis at pH 5.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 0.1 M Sodium citrate pH5.5
20 % w/v PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.149 α = 90 b = 83.149 β = 90 c = 87.488 γ = 120
Symmetry Space Group P 32 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 EIGER X 16M 2019-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976250 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.49 41.61 100 0.039 0.999 37.3 20.2 57478
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.52 100 1.238 0.88 3.3 20.2
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 (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 4XB5 1.49 41.6 54626 2826 99.91 0.1303 0.1284 0.1329 0.1672 0.172 RANDOM 32.465
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] 0.42 0.21 0.42 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.985 r_dihedral_angle_4_deg 21.918 r_rigid_bond_restr 14.101 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 6.061 r_angle_other_deg 1.383 r_angle_refined_deg 1.263 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.985 r_dihedral_angle_4_deg 21.918 r_rigid_bond_restr 14.101 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 6.061 r_angle_other_deg 1.383 r_angle_refined_deg 1.263 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2355 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 57
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing