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Crystal Structure of Pd(allyl)/apo-H114AFr
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 3.13 60.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.176 α = 90 b = 181.176 β = 90 c = 181.176 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 2007-07-03 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 1.75 30 99.1 0.061 6.7 26016 20.186
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) 1.75 1.81 98.6 0.302 5.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DAT 1.75 25.13 24666 1318 98.98 0.1789 0.17725 0.1761 0.21127 0.2106 RANDOM 19.411
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 37.146 r_sphericity_free 31.702 r_dihedral_angle_4_deg 17.435 r_dihedral_angle_3_deg 13.304 r_sphericity_bonded 5.023 r_dihedral_angle_1_deg 5.004 r_scangle_it 3.677 r_scbond_it 2.303 r_mcangle_it 1.309 r_angle_refined_deg 1.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.146 r_sphericity_free 31.702 r_dihedral_angle_4_deg 17.435 r_dihedral_angle_3_deg 13.304 r_sphericity_bonded 5.023 r_dihedral_angle_1_deg 5.004 r_scangle_it 3.677 r_scbond_it 2.303 r_mcangle_it 1.309 r_angle_refined_deg 1.181 r_mcbond_it 0.857 r_nbtor_refined 0.301 r_nbd_refined 0.218 r_symmetry_metal_ion_refined 0.207 r_metal_ion_refined 0.189 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1437 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing