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Apo-Fr with intermediate content of Pd ion
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 293 Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.09 60.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.57 α = 90 b = 180.57 β = 90 c = 180.57 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 ADSC QUANTUM 315 2006-03-03 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.5086 SPring-8 BL41XU 2 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.4639 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 1,2 2.1 50 100 0.086 70.5 42.7 15240 -3 23.099
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) 1,2 2.103 2.23 100 0.258 18.4 44.1
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 1DAT 2.1 40.39 14423 760 99.68 0.20179 0.19905 0.1991 0.25352 0.2494 RANDOM 25.279
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 35.467 r_dihedral_angle_4_deg 21.625 r_dihedral_angle_3_deg 16.34 r_dihedral_angle_1_deg 6.908 r_scangle_it 4.374 r_mcangle_it 3.249 r_scbond_it 2.894 r_mcbond_it 2.638 r_angle_refined_deg 1.489 r_symmetry_vdw_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.467 r_dihedral_angle_4_deg 21.625 r_dihedral_angle_3_deg 16.34 r_dihedral_angle_1_deg 6.908 r_scangle_it 4.374 r_mcangle_it 3.249 r_scbond_it 2.894 r_mcbond_it 2.638 r_angle_refined_deg 1.489 r_symmetry_vdw_refined 0.314 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.239 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1367 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALEPACK data scaling MOLREP phasing