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NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NIP PDB ENTRY 1NIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 liquid-liquid diffusion 8 PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD, USING 25-30% PEG 4000, 140-200 MM NA2MOO4, 100 MM TRIS-CL, PH 8.0; PROTEIN WAS HELD IN A BUFFER OF 20% GLYCEROL, 50 MM TRIS-CL, PH 8.0, 450 MM NACL, AND 2 MM NA2S2O4 PRIOR TO CRYSTALLIZATION., liquid-liquid diffusion
Crystal Properties Matthews coefficient Solvent content 2.4 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.12 α = 90 b = 90.53 β = 90 c = 91.21 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE MARRESEARCH MIRROR 1995-03-02 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
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 2.13 50 92.9 0.085 0.085 6.9 4 29060 35
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) 2.2 2.28 94.9 0.309 0.309 2.4 3.8
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 PDB ENTRY 1NIP 2.2 50 29180 1737 92.9 0.223 0.223 0.29 RANDOM 31.7
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] -19.79 -4.98 -11.26
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.9 x_scangle_it 5.18 x_mcangle_it 3.64 x_scbond_it 3.62 x_mcbond_it 2.4 x_angle_deg 1.9 x_improper_angle_d 1.64 x_bond_d 0.017 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.9 x_scangle_it 5.18 x_mcangle_it 3.64 x_scbond_it 3.62 x_mcbond_it 2.4 x_angle_deg 1.9 x_improper_angle_d 1.64 x_bond_d 0.017 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4356 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 8
Software Software Software Name Purpose AMoRE phasing X-PLOR refinement DENZO data reduction SCALEPACK data scaling