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Crystal structure of Pd(allyl)/polyhedra mutant with deletion of Gly192-Ala194
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 300 in vivo crystallization
Crystal Properties Matthews coefficient Solvent content 1.76 30.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.92 α = 90 b = 105.92 β = 90 c = 105.92 γ = 90
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 9M 2016-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.08 50 100 0.908 0.994 9.78 68.9 12029
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.21 100 14.8 0.386 0.95 69.1
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 5GQK 2.08 43.2 10839 1190 99.98 0.19371 0.18824 0.1953 0.24367 0.2458 RANDOM 36.449
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.41 r_dihedral_angle_3_deg 18.523 r_dihedral_angle_4_deg 16.436 r_long_range_B_refined 7.501 r_long_range_B_other 7.457 r_dihedral_angle_1_deg 7.359 r_scangle_other 5.815 r_mcangle_other 4.087 r_mcangle_it 4.084 r_scbond_it 3.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.41 r_dihedral_angle_3_deg 18.523 r_dihedral_angle_4_deg 16.436 r_long_range_B_refined 7.501 r_long_range_B_other 7.457 r_dihedral_angle_1_deg 7.359 r_scangle_other 5.815 r_mcangle_other 4.087 r_mcangle_it 4.084 r_scbond_it 3.774 r_scbond_other 3.773 r_mcbond_it 2.713 r_mcbond_other 2.687 r_angle_refined_deg 1.762 r_angle_other_deg 1.114 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1459 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHENIX phasing