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Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 complexed with imidazole
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. 0.25%(w/v) hexamminecobalt(III) chloride, 0.25%(w/v)
salicylamide, 0.25%(w/v) sulfanilamide, 0.25%(w/v) vanilic acid, 0.02 M HEPES sodium pH 6.8.
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.264 α = 90 b = 66.747 β = 116.5 c = 38.561 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 PIXEL PSI PILATUS 6M 2012-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.8 SLS X06SA
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 1.8 34.25 97.6 0.083 9.2 3.3 15836
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 1.8 1.85 96.9 0.439 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 1.8 34.245 2 15833 792 97.96 0.18 0.178 0.1741 0.217 0.2087
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] 9.9689 2.5951 -4.9168 -5.0521
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.049 f_angle_d 1.157 f_chiral_restr 0.088 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1461 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing