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Crystal Structure of 25Pd(allyl)/apo-Fr
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 3.14 60.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.52 α = 90 b = 181.52 β = 90 c = 181.52 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 1.58 30 99.9 0.083 12.1 35634 15.3
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) 1.58 1.64 100 0.285 12.3
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 1.58 25.17 33824 1786 99.87 0.19267 0.19168 0.1912 0.21179 0.2119 RANDOM 15.39
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 35.425 r_dihedral_angle_4_deg 20.426 r_sphericity_free 14.911 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 4.752 r_scangle_it 3.336 r_scbond_it 2.108 r_angle_refined_deg 1.314 r_mcangle_it 1.265 r_mcbond_it 0.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.425 r_dihedral_angle_4_deg 20.426 r_sphericity_free 14.911 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 4.752 r_scangle_it 3.336 r_scbond_it 2.108 r_angle_refined_deg 1.314 r_mcangle_it 1.265 r_mcbond_it 0.799 r_nbtor_refined 0.317 r_nbd_refined 0.262 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.09 r_symmetry_metal_ion_refined 0.019 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1364 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement SCALEPACK data scaling