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Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 complexed with NO
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) Gly-Gly, 0.25%(w/v) Gly-Gly-Gly, 0.25%(w/v) Gly-
Gly-Gly-Gly, 0.25%(w/v) pentaglycine, 0.02 M HEPES sodium pH 6.8.
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.887 α = 90 b = 67.052 β = 117.35 c = 39.082 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 1.0 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 1.29 34.71 94 0.032 9.5 1.7 83829
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 1.29 1.32 84 0.925 1 1.5
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 1.29 34.71 1.99 83819 4183 94.29 0.1723 0.1706 0.1677 0.2045 0.2008
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] -2.7207 1.0778 1.1001 1.6206
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.898 f_angle_d 1.074 f_chiral_restr 0.085 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1461 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing