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Crystal structure of L122V/L132V mutant of nitrophorin 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.74 28.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.44 α = 90 b = 126.34 β = 90 c = 33.96 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH bent Si-mirror 2003-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.1808 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.47 30 97 0.08 20.8 6.6 29090 29090 20.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.47 1.52 84 0.19 4.8 4.8 2489
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 1EUO 1.47 30 27616 27616 1474 97.06 0.13922 0.13922 0.13713 0.1384 0.1773 0.1772 RANDOM 11.765
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] 0.31 -0.11 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.004 r_dihedral_angle_3_deg 12.423 r_sphericity_free 10.312 r_dihedral_angle_1_deg 6.652 r_scangle_it 4.811 r_sphericity_bonded 3.928 r_scbond_it 3.744 r_dihedral_angle_4_deg 3.414 r_mcangle_it 2.504 r_mcbond_it 2.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.004 r_dihedral_angle_3_deg 12.423 r_sphericity_free 10.312 r_dihedral_angle_1_deg 6.652 r_scangle_it 4.811 r_sphericity_bonded 3.928 r_scbond_it 3.744 r_dihedral_angle_4_deg 3.414 r_mcangle_it 2.504 r_mcbond_it 2.088 r_angle_refined_deg 1.854 r_rigid_bond_restr 1.777 r_angle_other_deg 1.223 r_mcbond_other 0.774 r_symmetry_vdw_other 0.231 r_nbd_refined 0.23 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.18 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.119 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1487 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling