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Crystal Structure of Pd(allyl)/apo-C48AFr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.19 61.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.433 α = 90 b = 182.433 β = 90 c = 182.433 γ = 90
Symmetry Space Group F 4 3 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 CCD RAYONIX MX225HE 2009-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.5080 SPring-8 BL41XU
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 1.85 30 100 0.094 11.3 22730 16.771
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) 1.85 1.92 100 0.272 11.6
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 1DAT 1.85 25.55 21557 1162 99.93 0.17837 0.1771 0.1769 0.20283 0.2017 RANDOM 16.087
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 36.389 r_dihedral_angle_4_deg 17.119 r_sphericity_free 16.865 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 4.16 r_scangle_it 4.052 r_scbond_it 2.469 r_mcangle_it 1.412 r_angle_refined_deg 1.219 r_mcbond_it 0.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.389 r_dihedral_angle_4_deg 17.119 r_sphericity_free 16.865 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 4.16 r_scangle_it 4.052 r_scbond_it 2.469 r_mcangle_it 1.412 r_angle_refined_deg 1.219 r_mcbond_it 0.897 r_nbtor_refined 0.304 r_nbd_refined 0.218 r_symmetry_metal_ion_refined 0.211 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.12 r_metal_ion_refined 0.106 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1360 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement SCALEPACK data scaling