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1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D2U PDB entry 1D2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Ammonium Phosphate 2.8 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.149 α = 90 b = 42.804 β = 93.93 c = 52.881 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) 2002-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
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 0.99 21.4 98.8 0.049 0.049 27.3 4.62 85962 85962 6.62
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) 0.99 1.03 99.4 0.157 0.157 7.7 3.34 8609
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 1D2U 1 21.4 85962 77984 4104 97.27 0.1563 0.1563 0.15559 0.1575 0.1696 0.1599 RANDOM 8.691
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] -0.07 -0.03 0.05 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.532 r_sphericity_free 3.625 r_scangle_it 3.165 r_sphericity_bonded 2.915 r_scbond_it 2.155 r_mcangle_it 1.987 r_angle_refined_deg 1.66 r_mcbond_it 1.29 r_rigid_bond_restr 1.09 r_angle_other_deg 0.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.532 r_sphericity_free 3.625 r_scangle_it 3.165 r_sphericity_bonded 2.915 r_scbond_it 2.155 r_mcangle_it 1.987 r_angle_refined_deg 1.66 r_mcbond_it 1.29 r_rigid_bond_restr 1.09 r_angle_other_deg 0.794 r_nbd_other 0.254 r_symmetry_vdw_other 0.219 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.117 r_nbtor_other 0.11 r_chiral_restr 0.098 r_symmetry_hbond_refined 0.058 r_bond_refined_d 0.012 r_metal_ion_refined 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 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 1450 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection d*TREK data scaling