☰ Navigation Tabs
Apo-Fr with low 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 3.1 60.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.79 α = 90 b = 180.79 β = 90 c = 180.79 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 1.65 50 100 0.085 40 21.5 30995 -3 15.581
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 1.65 1.693 100 0.298 14.1 22.1
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 1.65 34.79 29369 1578 99.93 0.16959 0.1686 0.1681 0.18788 0.1861 RANDOM 17.148
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 38.068 r_dihedral_angle_4_deg 16.13 r_dihedral_angle_3_deg 12.914 r_dihedral_angle_1_deg 4.241 r_sphericity_free 2.996 r_scangle_it 2.949 r_scbond_it 1.934 r_angle_refined_deg 1.144 r_mcangle_it 1.021 r_mcbond_it 0.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.068 r_dihedral_angle_4_deg 16.13 r_dihedral_angle_3_deg 12.914 r_dihedral_angle_1_deg 4.241 r_sphericity_free 2.996 r_scangle_it 2.949 r_scbond_it 1.934 r_angle_refined_deg 1.144 r_mcangle_it 1.021 r_mcbond_it 0.683 r_nbtor_refined 0.303 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.21 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1369 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALEPACK data scaling MOLREP phasing