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Crystal structure of a far-red light-absorbing form of AnPixJg2_BV4 in complex with biliverdin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 0.1 M sodium cacodylate, 26% PEG 3350, 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.32 47.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.957 α = 90 b = 60.65 β = 108.59 c = 55.475 γ = 90
Symmetry Space Group C 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 100 CCD ADSC QUANTUM 270 2017-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 50 98 0.041 28.2 3.6 27039
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 99.9 0.388 3.1 3.7
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 3W2Z 1.6 31.67 25495 1346 97.91 0.20785 0.20607 0.2198 0.24075 0.2511 RANDOM 26.308
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.995 r_dihedral_angle_4_deg 19.113 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 6.188 r_long_range_B_refined 6.176 r_long_range_B_other 6.119 r_scangle_other 3.926 r_mcangle_it 3.501 r_mcangle_other 3.499 r_scbond_it 2.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.995 r_dihedral_angle_4_deg 19.113 r_dihedral_angle_3_deg 12.129 r_dihedral_angle_1_deg 6.188 r_long_range_B_refined 6.176 r_long_range_B_other 6.119 r_scangle_other 3.926 r_mcangle_it 3.501 r_mcangle_other 3.499 r_scbond_it 2.412 r_scbond_other 2.402 r_mcbond_it 2.162 r_mcbond_other 2.136 r_angle_refined_deg 2.083 r_angle_other_deg 0.885 r_chiral_restr 0.093 r_gen_planes_other 0.017 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1417 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing