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1.0 A Crystal Structure of T121V Mutant of Nitrophorin 4 Complexed with Nitric Oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KOI PDB entry 1KOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.395 α = 90 b = 42.724 β = 94.31 c = 53.032 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 ADSC QUANTUM 315 Flat mirror (vertical focusing) 2002-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.751 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.01 30.6 96.1 0.043 0.043 16.6 3.66 80037 80037 3.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.01 1.04 88.6 0.175 0.175 6.2 3.46 7313
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1KOI 1.01 26.44 80037 75071 3967 96.06 0.13006 0.13006 0.1293 0.14452 0.1371 RANDOM 6.09
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] 0.01 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.45 r_sphericity_free 4.162 r_scangle_it 3.088 r_sphericity_bonded 2.734 r_angle_other_deg 2.576 r_scbond_it 2.137 r_mcangle_it 1.775 r_angle_refined_deg 1.729 r_mcbond_it 1.172 r_rigid_bond_restr 1.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.45 r_sphericity_free 4.162 r_scangle_it 3.088 r_sphericity_bonded 2.734 r_angle_other_deg 2.576 r_scbond_it 2.137 r_mcangle_it 1.775 r_angle_refined_deg 1.729 r_mcbond_it 1.172 r_rigid_bond_restr 1.093 r_metal_ion_refined 0.38 r_symmetry_vdw_other 0.269 r_nbd_other 0.251 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.103 r_nbtor_other 0.089 r_gen_planes_other 0.022 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1448 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection d*TREK data scaling