☰ Navigation Tabs
Crystal structure of a bacterial immunoglobulin-like domain from the M. primoryensis ice-binding adhesin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KDV PDB ENTRY 4KDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 298 20% PEG 4000, 0.2M CaCl2, 0.1M Tris-HCl, microbatch, pH 8.5, EVAPORATION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.72 28.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.64 α = 97.02 b = 28.62 β = 112.93 c = 32.25 γ = 96.88
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 300 mm CCD 2012-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 1.35 29.191 95.1 0.049 10.33 3.6 17224 7.4
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) 1 1.35 1.42 91.6 0.085 10.7 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4KDV 1.35 29.19 16337 16337 887 95.1 0.132 0.13 0.165 0.1938 RANDOM 9.71
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] 0.54 0.21 0.06 0.03 0.21 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.989 r_dihedral_angle_3_deg 8.704 r_dihedral_angle_1_deg 6.228 r_angle_refined_deg 2.244 r_angle_other_deg 0.927 r_chiral_restr 0.128 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.989 r_dihedral_angle_3_deg 8.704 r_dihedral_angle_1_deg 6.228 r_angle_refined_deg 2.244 r_angle_other_deg 0.927 r_chiral_restr 0.128 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 691 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 13
Software Software Software Name Purpose JBluIce-EPICS data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling