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Crystal Structure of Pd(allyl)/apo-E45C/R52H-rHLFr
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, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.14 60.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.427 α = 90 b = 181.427 β = 90 c = 181.427 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 2009-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 1.52 25 99.2 0.054 10.2 39501
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) 1.52 1.57 93.9 0.347 5.5
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 1.52 19.34 37012 1951 97.96 0.19648 0.19584 0.1931 0.20867 0.2067 RANDOM 18.485
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 36.06 r_dihedral_angle_4_deg 19.518 r_dihedral_angle_3_deg 14.715 r_dihedral_angle_1_deg 4.457 r_scangle_it 3.207 r_scbond_it 1.919 r_angle_refined_deg 1.592 r_mcangle_it 1.174 r_mcbond_it 0.606 r_chiral_restr 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.06 r_dihedral_angle_4_deg 19.518 r_dihedral_angle_3_deg 14.715 r_dihedral_angle_1_deg 4.457 r_scangle_it 3.207 r_scbond_it 1.919 r_angle_refined_deg 1.592 r_mcangle_it 1.174 r_mcbond_it 0.606 r_chiral_restr 0.239 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1380 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 66
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement SCALEPACK data scaling