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1.4 A Crystal Structure of D30N Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Imidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.135 α = 90 b = 42.541 β = 94.12 c = 52.995 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 IMAGE PLATE RIGAKU RAXIS IV 2001-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.36 20.4 99.3 0.034 0.034 20.3 2.53 33304 33304 8.93
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) 1.36 1.41 96.3 0.07 0.07 7.7 1.31 3213
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 1IKJ 1.4 20.4 33304 29297 1539 99.97 0.14264 0.14264 0.14092 0.1474 0.17534 0.1392 RANDOM 12.055
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] -0.08 -0.09 -0.09 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.862 r_sphericity_free 5.552 r_scangle_it 4.626 r_sphericity_bonded 3.585 r_scbond_it 3.228 r_mcangle_it 2.569 r_angle_refined_deg 1.816 r_mcbond_it 1.67 r_rigid_bond_restr 1.661 r_symmetry_vdw_refined 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.862 r_sphericity_free 5.552 r_scangle_it 4.626 r_sphericity_bonded 3.585 r_scbond_it 3.228 r_mcangle_it 2.569 r_angle_refined_deg 1.816 r_mcbond_it 1.67 r_rigid_bond_restr 1.661 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.126 r_symmetry_hbond_refined 0.092 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1447 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling