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Atomic Resolution Structure of the Wildtype Native Nitrite Reductase from Alcaligenes xylosoxidans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HAU PDB ENTRY 1HAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 40-50% PEG-MME 550, 0.1M MES PH 6.5, 10MM CUSO4
Crystal Properties Matthews coefficient Solvent content 2.4 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.725 α = 90 b = 78.725 β = 90 c = 98.885 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 100 CCD ADSC CCD MIRRORS 2001-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 1.04 60 96.6 0.075 19.1 10.6 167110
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 1.04 1.06 93.1 0.33 2.3 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HAU 1.04 60 162462 3245 97.9 0.1175 0.1193 0.1416 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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 18 3106
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.099 s_zero_chiral_vol 0.093 s_approx_iso_adps 0.087 s_from_restr_planes 0.0352 s_similar_adp_cmpnt 0.035 s_angle_d 0.032 s_bond_d 0.017 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2548 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 15
Software Software Software Name Purpose SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing