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Outer membrane protein from Vibrio campbellii 25 kDa (OmpV25)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 0.05 M Lithium phosphate
0.025 M Sodium acetate
pH 5.0
23% v/v PEG 300
Crystal Properties Matthews coefficient Solvent content 3.18 61.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.54 α = 90 b = 77.089 β = 95.09 c = 143.062 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 CCD MARMOSAIC 300 mm CCD LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors 2022-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 50 99.1 0.086 0.032 0.786 6.4 7 34012 49.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 89 0.479 0.544 0.249 0.786 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2.7 38.21 1.38 33980 1629 98.88 0.2119 0.2092 0.211 0.2678 0.269
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.423 f_angle_d 0.959 f_chiral_restr 0.052 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6533 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 259
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction PHENIX phasing