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Crystal structure of Ca2+-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 6.5 293 50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.17 61.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.78 α = 90 b = 154.425 β = 90 c = 237.676 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 2006-03-10 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 3.1 118.68 99.99 0.094 6.7 7 37803
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) 3.1 3.21 98.4 0.309 6.4 3679
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 3.1 50 33903 3769 99.99 0.22757 0.22178 0.2254 0.27976 0.2798 RANDOM 42.061
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] -0.09 0.11 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.299 r_dihedral_angle_3_deg 20.919 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_1_deg 6.122 r_angle_refined_deg 1.138 r_scangle_it 0.798 r_mcangle_it 0.511 r_scbond_it 0.457 r_nbtor_refined 0.318 r_symmetry_hbond_refined 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.299 r_dihedral_angle_3_deg 20.919 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_1_deg 6.122 r_angle_refined_deg 1.138 r_scangle_it 0.798 r_mcangle_it 0.511 r_scbond_it 0.457 r_nbtor_refined 0.318 r_symmetry_hbond_refined 0.285 r_mcbond_it 0.281 r_symmetry_vdw_refined 0.278 r_nbd_refined 0.253 r_metal_ion_refined 0.225 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.084 r_bond_refined_d 0.008 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 10931 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing