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crystal structure of nitrate-reducing fragment of assimilatory nitrate reductase from Pichia angusta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIH PDB ENTRY 2BIH
Crystallization Crystal Properties Matthews coefficient Solvent content 2.9 57.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.722 α = 90 b = 123.08 β = 90 c = 149.509 γ = 90
Symmetry Space Group C 2 2 21
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 MIRRORS 2003-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
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 1.7 25 99 0.09 4.6 4.3 2235039
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 1.7 1.79 99.8 0.51 1.6 2.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BIH 1.7 87.71 116173 6133 98.8 0.186 0.185 0.1813 0.212 0.2083 RANDOM 24.68
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] 0.58 0.93 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.45 r_dihedral_angle_4_deg 17.712 r_dihedral_angle_3_deg 13.031 r_dihedral_angle_1_deg 5.892 r_scangle_it 3.928 r_scbond_it 2.59 r_angle_refined_deg 1.996 r_mcangle_it 1.558 r_mcbond_it 0.862 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.45 r_dihedral_angle_4_deg 17.712 r_dihedral_angle_3_deg 13.031 r_dihedral_angle_1_deg 5.892 r_scangle_it 3.928 r_scbond_it 2.59 r_angle_refined_deg 1.996 r_mcangle_it 1.558 r_mcbond_it 0.862 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.264 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.132 r_gen_planes_refined 0.038 r_bond_refined_d 0.018 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 6704 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing