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Apo-Fr with high content of Pd ions
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 3.14 60.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.594 α = 90 b = 181.594 β = 90 c = 181.594 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 1 100 CCD ADSC QUANTUM 315 2006-03-03
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 2.5 50 100 0.092 33.9 11.6 9397 -3 39.084
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) 2.5 2.69 100 0.302 7.2 11.8
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 2.5 45.41 8894 503 99.96 0.22298 0.21943 0.2147 0.28671 0.277 RANDOM 31.593
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 39.964 r_dihedral_angle_4_deg 27.738 r_dihedral_angle_3_deg 21.981 r_sphericity_free 19.109 r_dihedral_angle_1_deg 11.829 r_scangle_it 6.356 r_scbond_it 4.155 r_mcangle_it 2.451 r_angle_refined_deg 2.262 r_mcbond_it 1.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.964 r_dihedral_angle_4_deg 27.738 r_dihedral_angle_3_deg 21.981 r_sphericity_free 19.109 r_dihedral_angle_1_deg 11.829 r_scangle_it 6.356 r_scbond_it 4.155 r_mcangle_it 2.451 r_angle_refined_deg 2.262 r_mcbond_it 1.495 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.307 r_metal_ion_refined 0.305 r_nbd_refined 0.274 r_symmetry_vdw_refined 0.225 r_chiral_restr 0.202 r_xyhbond_nbd_refined 0.162 r_bond_refined_d 0.026 r_gen_planes_refined 0.01 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_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_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1366 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALEPACK data scaling MOLREP phasing