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Crystal structure of Zn2+-bound form of des3-20ALG-2F122A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZN8 PDB ENTRY 2ZN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 25% 2-methyl-2,4-pentanediol, 100mM Cacodylate, 50mM Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.54 65.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.266 α = 90 b = 170.209 β = 90 c = 46.911 γ = 90
Symmetry Space Group C 2 2 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 210r 2008-11-12 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 2.5 50 97.3 0.043 28.8 3.8 10302
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 2.59 88.4 0.12 14.3 3.6
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 2ZN8 2.7 32.24 7738 389 98.93 0.25422 0.25206 0.2489 0.29827 0.2983 RANDOM 56.294
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] 10.75 -5.21 -5.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.994 r_dihedral_angle_4_deg 20.541 r_dihedral_angle_3_deg 15.856 r_dihedral_angle_1_deg 4.156 r_angle_refined_deg 0.858 r_scangle_it 0.845 r_mcangle_it 0.56 r_scbond_it 0.49 r_mcbond_it 0.313 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.994 r_dihedral_angle_4_deg 20.541 r_dihedral_angle_3_deg 15.856 r_dihedral_angle_1_deg 4.156 r_angle_refined_deg 0.858 r_scangle_it 0.845 r_mcangle_it 0.56 r_scbond_it 0.49 r_mcbond_it 0.313 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.209 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.138 r_metal_ion_refined 0.07 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 1385 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 3
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling