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Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 25%(w/v) PEG 3350, 0.1 M bis-Tris propane pH 7.8, 0.02 M HEPES pH 6.8, 0.25%(w/v) naphthalene-1,3,6-trisulfonic
acid trisodium salt hydrate, 0.25%(w/v) 2,6-naphthalenedisulfonic acid disodium salt, 0.25%(w/v) 4-aminobenzoic acid,
0.25%(w/v) 5-sulfosalicylic acid dehydrate.
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.312 α = 90 b = 66.807 β = 116.87 c = 39.026 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225HE 2011-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.6 30.42 99.4 0.04 20.5 3.8 23143
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 1.6 1.64 99.8 0.486 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 3MVF 1.6 30.42 2 23137 1158 99.78 0.1376 0.1347 0.1395 0.1916 0.19
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 14.069 f_angle_d 1.026 f_chiral_restr 0.045 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1461 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing