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sulerythrin without metals (apo-state)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1 M Bis-Tris (pH 5.5) and 20-25% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 3.34 63.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.147 α = 90 b = 96.147 β = 90 c = 80.688 γ = 120
Symmetry Space Group P 63 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 PILATUS3 S 6M 2016-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.16 48.07 99.92 0.075 1 20.1 12.81 974906
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 1.16 1.2 0.617
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 1J30 1.16 48.07 74017 2101 99.91 0.12459 0.12399 0.1276 0.14603 0.1478 RANDOM 16.954
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] 0.13 0.06 0.13 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.55 r_dihedral_angle_4_deg 14.807 r_dihedral_angle_3_deg 12.163 r_long_range_B_refined 4.568 r_dihedral_angle_1_deg 4.178 r_long_range_B_other 3.804 r_scangle_other 3.147 r_rigid_bond_restr 3.039 r_scbond_it 2.71 r_scbond_other 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.55 r_dihedral_angle_4_deg 14.807 r_dihedral_angle_3_deg 12.163 r_long_range_B_refined 4.568 r_dihedral_angle_1_deg 4.178 r_long_range_B_other 3.804 r_scangle_other 3.147 r_rigid_bond_restr 3.039 r_scbond_it 2.71 r_scbond_other 2.71 r_angle_refined_deg 1.827 r_mcangle_other 1.816 r_mcangle_it 1.795 r_angle_other_deg 1.741 r_mcbond_it 1.312 r_mcbond_other 1.281 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1109 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing