☰ Navigation Tabs
Crystal structure of E55Q mutant of nitrophorin 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.379 α = 90 b = 42.838 β = 94.2 c = 53.056 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 4 mirrors 2008-02-24 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) 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 30.6 95.58 0.081 10.3 3.17 23089
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) 1.5 1.55 100 0.295 2.7 3.15 2527
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 1D2U 1.5 30 23089 23089 1220 95.58 0.171 0.171 0.16886 0.1777 0.20123 0.2089 RANDOM 10.663
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] -0.04 0.48 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.51 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_1_deg 7.084 r_dihedral_angle_4_deg 6.563 r_scangle_it 3.24 r_scbond_it 2.516 r_mcangle_it 1.551 r_angle_refined_deg 1.501 r_angle_other_deg 1.405 r_mcbond_it 1.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.51 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_1_deg 7.084 r_dihedral_angle_4_deg 6.563 r_scangle_it 3.24 r_scbond_it 2.516 r_mcangle_it 1.551 r_angle_refined_deg 1.501 r_angle_other_deg 1.405 r_mcbond_it 1.285 r_mcbond_other 0.241 r_nbd_refined 0.223 r_symmetry_vdw_other 0.203 r_nbd_other 0.19 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.115 r_symmetry_hbond_refined 0.114 r_nbtor_other 0.087 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_metal_ion_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1476 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection REFMAC refinement CrystalClear data reduction CrystalClear data scaling REFMAC phasing