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Crystal structure of the N-terminal 1-37 residues deleted mutant of Geobacillus copper nitrite reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.1M Hepes-NaOH, 2.0M Ammonium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.19 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.317 α = 90 b = 164.991 β = 102.27 c = 126.561 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX225HE 2012-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.77 124 98.6 346257 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 98.4
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 3WI9 1.77 42.7 323635 17225 98.4 0.1723 0.17123 0.171 0.19243 0.1913 RANDOM 25.881
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] 1.22 -1.56 -0.81 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.521 r_dihedral_angle_3_deg 13.201 r_dihedral_angle_4_deg 9.421 r_dihedral_angle_1_deg 7.807 r_scangle_it 3.523 r_scbond_it 2.193 r_angle_refined_deg 1.435 r_mcangle_it 1.252 r_mcbond_it 0.694 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.521 r_dihedral_angle_3_deg 13.201 r_dihedral_angle_4_deg 9.421 r_dihedral_angle_1_deg 7.807 r_scangle_it 3.523 r_scbond_it 2.193 r_angle_refined_deg 1.435 r_mcangle_it 1.252 r_mcbond_it 0.694 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19178 Nucleic Acid Atoms Solvent Atoms 2029 Heterogen Atoms 72
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling