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Crystal Structure of Pd(allyl)/apo-H49AFr
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 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.14 60.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.339 α = 90 b = 181.339 β = 90 c = 181.339 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 IMAGE PLATE RIGAKU RAXIS VII 2007-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.6 50 100 0.062 17.8 34183 18.007
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) 1.6 1.66 100 0.284 8.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DAT 1.6 25.15 32427 1728 99.94 0.18869 0.18751 0.2111 0.2236 RANDOM 18.223
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 36.275 r_dihedral_angle_4_deg 21.302 r_sphericity_free 16.524 r_dihedral_angle_3_deg 14.255 r_sphericity_bonded 7.833 r_dihedral_angle_1_deg 4.429 r_scangle_it 3.398 r_scbond_it 2.08 r_mcangle_it 1.181 r_angle_refined_deg 1.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.275 r_dihedral_angle_4_deg 21.302 r_sphericity_free 16.524 r_dihedral_angle_3_deg 14.255 r_sphericity_bonded 7.833 r_dihedral_angle_1_deg 4.429 r_scangle_it 3.398 r_scbond_it 2.08 r_mcangle_it 1.181 r_angle_refined_deg 1.098 r_mcbond_it 0.687 r_nbtor_refined 0.305 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1451 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing