☰ Navigation Tabs
Crystal structure of M144A mutant of Alcaligenes xylosoxidans Nitrite Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NDT PDN ENTRY 1NDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 30% PEG 4000, 0.1M MGCL2, 0.1M TRIS-HCL PH8.5, TEMP GRADIENT 4-32 DEGREES C, pH 8.50
Crystal Properties Matthews coefficient Solvent content 3.07 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.86 α = 90 b = 106.86 β = 90 c = 64.026 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 294 CCD ADSC CCD RH COATED SI MIRROR 1999-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 2.2 20 99.4 0.097 11.2 2.9 27656 2
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 2.2 2.32 99.4 0.32 2.4 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDN ENTRY 1NDT 2.2 60 20082 1058 99.2 0.15 0.148 0.181 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.417 r_scbond_it 3.764 r_mcangle_it 2.604 r_angle_other_deg 2.508 r_mcbond_it 1.557 r_dihedral_angle_3_deg 1.525 r_nbtor_other 0.22 r_nbd_other 0.213 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.205
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.417 r_scbond_it 3.764 r_mcangle_it 2.604 r_angle_other_deg 2.508 r_mcbond_it 1.557 r_dihedral_angle_3_deg 1.525 r_nbtor_other 0.22 r_nbd_other 0.213 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.205 r_xyhbond_nbd_other 0.197 r_symmetry_vdw_other 0.185 r_chiral_restr 0.18 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.142 r_metal_ion_refined 0.07 r_bond_refined_d 0.033 r_gen_planes_refined 0.016 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2572 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling AMoRE phasing