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Crystal structure of Zn2+-bound form of ALG-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 6.5 293 25% 2-methyl-2,4-pentanediol, 100mM Cacodylate, 75mM Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.25 62.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.01 α = 90 b = 169.738 β = 90 c = 46.343 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 315 2007-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.7 50 98.35 0.066 20.5 6.8 8147
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) 2.7 2.8 93.1 0.13 14.1 6.5
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 PDB ENTRY 1HQV 2.7 32.1 7653 372 98.35 0.21333 0.21111 0.2114 0.26022 0.2624 RANDOM 42.63
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] 7.26 -3.91 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.748 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_3_deg 18.333 r_dihedral_angle_1_deg 5.569 r_scangle_it 2.396 r_scbond_it 1.33 r_angle_refined_deg 1.126 r_mcangle_it 0.973 r_mcbond_it 0.488 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.748 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_3_deg 18.333 r_dihedral_angle_1_deg 5.569 r_scangle_it 2.396 r_scbond_it 1.33 r_angle_refined_deg 1.126 r_mcangle_it 0.973 r_mcbond_it 0.488 r_nbtor_refined 0.311 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.212 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.088 r_metal_ion_refined 0.053 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 1382 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing