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Crystal structure of heme-binding protein from Populus trichocarpa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 20% PEG monomethyl ether 2000, 10 mM nickel chloride and 100 mM sodium acetate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.306 α = 90 b = 77.306 β = 90 c = 92.42 γ = 90
Symmetry Space Group P 42 21 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 2020-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979 NSLS-II 17-ID-2
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 1.8 50 96.7 0.059 0.061 1 10.9 20 25732
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 1.8 1.85 79.5 1.03 0.647 2 8.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.8 38.68 24413 1262 96.62 0.20881 0.20644 0.2126 0.2547 0.266 RANDOM 42.387
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] -0.7 -0.7 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.076 r_dihedral_angle_3_deg 15.525 r_dihedral_angle_4_deg 10.968 r_long_range_B_other 10.437 r_long_range_B_refined 10.436 r_dihedral_angle_1_deg 7.372 r_scangle_other 7.143 r_mcangle_other 6.131 r_mcangle_it 6.129 r_scbond_it 4.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.076 r_dihedral_angle_3_deg 15.525 r_dihedral_angle_4_deg 10.968 r_long_range_B_other 10.437 r_long_range_B_refined 10.436 r_dihedral_angle_1_deg 7.372 r_scangle_other 7.143 r_mcangle_other 6.131 r_mcangle_it 6.129 r_scbond_it 4.579 r_scbond_other 4.577 r_mcbond_it 4.055 r_mcbond_other 4.048 r_angle_refined_deg 1.646 r_angle_other_deg 1.34 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2062 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing