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1.0 A Crystal Structure of D129A/L130A 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 37.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.219 α = 90 b = 42.751 β = 94.3 c = 53.055 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) 2002-02-20 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 97.1 0.049 0.049 18.5 4.1 80684 80684 4.92
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 89.2 0.239 0.239 5.2 3.46 7370
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1KOI 1.01 30.57 80684 76166 4036 96.5 0.14123 0.14123 0.1405 0.1429 0.15498 0.1419 RANDOM 7.307
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 r_dihedral_angle_1_deg 7.253 r_sphericity_free 4.057 r_scangle_it 3.133 r_sphericity_bonded 2.668 r_scbond_it 2.138 r_angle_other_deg 2.074 r_mcangle_it 1.808 r_angle_refined_deg 1.703 r_mcbond_it 1.209 r_rigid_bond_restr 1.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.253 r_sphericity_free 4.057 r_scangle_it 3.133 r_sphericity_bonded 2.668 r_scbond_it 2.138 r_angle_other_deg 2.074 r_mcangle_it 1.808 r_angle_refined_deg 1.703 r_mcbond_it 1.209 r_rigid_bond_restr 1.109 r_metal_ion_refined 0.398 r_nbd_refined 0.286 r_symmetry_vdw_other 0.254 r_nbd_other 0.252 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.105 r_nbtor_other 0.09 r_symmetry_hbond_refined 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1474 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection d*TREK data scaling