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Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DDB PDB ENTRY 2DDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 3.6M SODIUM FORMATE, 10%(W/V) GLYCEROL, 0.15M NACL, 50MM TRIS-HCL, 3MM ZN ACETATE, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.077 α = 90 b = 62.344 β = 90 c = 246.943 γ = 90
Symmetry Space Group P 21 21 21
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 210 2005-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.3 50 99.4 0.088 10.7 6.9 42142 39.377
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) 2.3 2.38 95.2 0.394 3.7 5.9 3945
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 PDB ENTRY 2DDB 2.3 38.72 39944 2122 100 0.22156 0.2186 0.2122 0.27717 0.2708 RANDOM 35.405
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] -0.07 1.99 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.241 r_dihedral_angle_4_deg 21.386 r_dihedral_angle_3_deg 15.987 r_dihedral_angle_1_deg 5.431 r_scangle_it 2.097 r_scbond_it 1.301 r_angle_refined_deg 1.14 r_mcangle_it 0.929 r_mcbond_it 0.485 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.241 r_dihedral_angle_4_deg 21.386 r_dihedral_angle_3_deg 15.987 r_dihedral_angle_1_deg 5.431 r_scangle_it 2.097 r_scbond_it 1.301 r_angle_refined_deg 1.14 r_mcangle_it 0.929 r_mcbond_it 0.485 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.083 r_metal_ion_refined 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6496 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing