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Crystal structure of nitrophorin 2 L122V/L132V mutant complex with imidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUO PDB entry 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 2.08 40.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.31 α = 90 b = 125.47 β = 90 c = 33.88 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 ADSC QUANTUM 4 bent Si-mirror 2003-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 APS 14-BM-C
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 1.1 28.7 91 0.077 0.089 9.3 3.8 62884 62884 8.4
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) 1.1 1.14 81.2 0.27 0.27 1 3.1 5509
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 1EUO 1.1 28.64 62884 58988 3164 89.94 0.1547 0.1547 0.1536 0.1567 0.177 0.1568 RANDOM 10.562
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] 0.56 -0.43 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.982 r_sphericity_free 6.979 r_scangle_it 4.479 r_sphericity_bonded 4.297 r_scbond_it 3.184 r_mcangle_it 2.611 r_angle_other_deg 2.021 r_rigid_bond_restr 1.945 r_angle_refined_deg 1.936 r_mcbond_it 1.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.982 r_sphericity_free 6.979 r_scangle_it 4.479 r_sphericity_bonded 4.297 r_scbond_it 3.184 r_mcangle_it 2.611 r_angle_other_deg 2.021 r_rigid_bond_restr 1.945 r_angle_refined_deg 1.936 r_mcbond_it 1.871 r_nbd_other 0.266 r_symmetry_vdw_other 0.243 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.191 r_chiral_restr 0.157 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.103 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1419 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling