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Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 28% (w/v) PEG 400,
0.5 M potassium iodide,
0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 4.31 71.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 254.761 α = 90 b = 147.031 β = 95.51 c = 53.759 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979490 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.08 29.21 95.7 0.108 0.1 6.6 2.7 34933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.08 3.23 38.5 0.41 0.385 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5MDO 3.08 127.2 33200 1731 95.48 0.2181 0.21699 0.23977 0.2277 RANDOM 70.514
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] 1.55 -2.13 -1.74 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.068 r_dihedral_angle_4_deg 18.112 r_dihedral_angle_3_deg 17.537 r_dihedral_angle_1_deg 8.778 r_angle_refined_deg 2.17 r_long_range_B_refined 1.491 r_long_range_B_other 1.491 r_angle_other_deg 1.256 r_scangle_other 0.783 r_mcangle_it 0.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.068 r_dihedral_angle_4_deg 18.112 r_dihedral_angle_3_deg 17.537 r_dihedral_angle_1_deg 8.778 r_angle_refined_deg 2.17 r_long_range_B_refined 1.491 r_long_range_B_other 1.491 r_angle_other_deg 1.256 r_scangle_other 0.783 r_mcangle_it 0.753 r_mcangle_other 0.753 r_scbond_it 0.476 r_scbond_other 0.476 r_mcbond_it 0.423 r_mcbond_other 0.423 r_chiral_restr 0.105 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7995 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing