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Crystal structure of Nitrophorin 4 from Rhodnius prolixus Complexed with sulfide ion at pH 7.4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MVF PDB ENTRY 3MVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 3.2M AMMONIUM PHOSPHATE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.93 36.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.169 α = 90 b = 42.893 β = 94.05 c = 52.255 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 RAYONIX MX225HE 2011-03-15 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) 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 1.5 30.5 98.9 24703 -3 11.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 97.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3MVF 1.5 19.833 1.99 24695 24695 1235 98.89 0.136 0.136 0.1336 0.1277 0.1814 0.1752 RANDOM 16.614
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] 2.3167 2.0308 0.2526 -2.5693
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.824 f_angle_d 1.156 f_chiral_restr 0.078 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1428 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 44
Software Software Software Name Purpose XDS data scaling PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling