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Crystal structure of Zn2+-bound form of des3-23ALG-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HQV PDB ENTRY 1HQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.806 α = 90 b = 147.537 β = 90 c = 230.735 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 315 2006-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.28192 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 3.3 115.47 99.5 0.102 8 8.8 27970
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) 3.3 3.42 96.6 0.343 6 2610
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 1HQV 3.3 115.47 25283 2785 100 0.17411 0.16901 0.1684 0.22077 0.2174 RANDOM 99.308
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] 0.32 -0.87 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.133 r_dihedral_angle_3_deg 17.637 r_dihedral_angle_4_deg 16.237 r_dihedral_angle_1_deg 4.507 r_angle_refined_deg 0.89 r_scangle_it 0.779 r_mcangle_it 0.545 r_scbond_it 0.447 r_nbtor_refined 0.309 r_mcbond_it 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.133 r_dihedral_angle_3_deg 17.637 r_dihedral_angle_4_deg 16.237 r_dihedral_angle_1_deg 4.507 r_angle_refined_deg 0.89 r_scangle_it 0.779 r_mcangle_it 0.545 r_scbond_it 0.447 r_nbtor_refined 0.309 r_mcbond_it 0.298 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.147 r_metal_ion_refined 0.129 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.065 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 10967 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing