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Crystal structure of cold-aminopeptidase from Colwellia psychrerythraea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 23 % w/v PEG 3350, 0.5 M NaCl, 0.1 M Bis-Tris, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.37 α = 88.83 b = 87.1 β = 70.68 c = 116.36 γ = 88.43
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9799 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 46.7 93.5 0.2 0.09 8.57 2.29 80533 74827 2 1 37.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 67.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1HS6 2.7 46.68 80533 76497 4034 97.29 0.25047 0.24943 0.2497 0.27011 0.2706 RANDOM 32.193
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] 0.12 -0.08 0.05 -0.29 0.15 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.032 r_dihedral_angle_4_deg 18.715 r_dihedral_angle_3_deg 18.562 r_dihedral_angle_1_deg 6.553 r_scangle_it 2.385 r_angle_refined_deg 2.228 r_mcangle_it 2.097 r_scbond_it 1.544 r_mcbond_it 1.172 r_symmetry_hbond_refined 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.032 r_dihedral_angle_4_deg 18.715 r_dihedral_angle_3_deg 18.562 r_dihedral_angle_1_deg 6.553 r_scangle_it 2.385 r_angle_refined_deg 2.228 r_mcangle_it 2.097 r_scbond_it 1.544 r_mcbond_it 1.172 r_symmetry_hbond_refined 0.4 r_symmetry_vdw_refined 0.359 r_nbtor_refined 0.346 r_nbd_refined 0.314 r_xyhbond_nbd_refined 0.254 r_chiral_restr 0.168 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 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_refined 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 18685 Nucleic Acid Atoms Solvent Atoms 919 Heterogen Atoms 4
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction