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Crystal structure of Ca2+-bound form of des3-20ALG-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, SITTING DROP 6.5 293 18% PEG 8000, 0.1M Sodium Cacodylate, 0.2M Calcium Acetate hydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.024 α = 90 b = 72.024 β = 90 c = 91.663 γ = 90
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 4 2006-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
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 2.4 50 99.8 0.065 11.8 18354
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) 2.4 2.5 100 0.461 8.2
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 2.4 38.66 17411 941 99.76 0.23749 0.23433 0.2318 0.29843 0.2985 RANDOM 48.565
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] 0.42 0.42 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.045 r_dihedral_angle_4_deg 22.496 r_dihedral_angle_3_deg 18.185 r_dihedral_angle_1_deg 5.425 r_scangle_it 2.404 r_scbond_it 1.537 r_angle_refined_deg 1.339 r_mcangle_it 1.077 r_mcbond_it 0.594 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.045 r_dihedral_angle_4_deg 22.496 r_dihedral_angle_3_deg 18.185 r_dihedral_angle_1_deg 5.425 r_scangle_it 2.404 r_scbond_it 1.537 r_angle_refined_deg 1.339 r_mcangle_it 1.077 r_mcbond_it 0.594 r_nbtor_refined 0.311 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.172 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.148 r_metal_ion_refined 0.136 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_symmetry_metal_ion_refined 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_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 2816 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing