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Crystal Structure of Mutant NikA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 5.5 293 PEG 4000, ammonium sulfate, sodium iodide, nickel chloride, pH 5.5, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.47 α = 90 b = 92.248 β = 90 c = 116.383 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 95 CCD ADSC QUANTUM 315 2006-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.65 50 95.9 0.054 8.5 54989
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) 1.65 1.71 75.5 0.205 4247
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 1uiv 1.65 19.82 54867 2788 100 0.179 0.177 0.1875 0.21 0.2171 RANDOM 14.809
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] 0.02 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.128 r_dihedral_angle_4_deg 20.01 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 6.2 r_scangle_it 4.081 r_scbond_it 2.68 r_mcangle_it 1.559 r_angle_refined_deg 1.546 r_mcbond_it 0.9 r_angle_other_deg 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.128 r_dihedral_angle_4_deg 20.01 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 6.2 r_scangle_it 4.081 r_scbond_it 2.68 r_mcangle_it 1.559 r_angle_refined_deg 1.546 r_mcbond_it 0.9 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.284 r_mcbond_other 0.25 r_nbd_refined 0.232 r_nbd_other 0.195 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.14 r_symmetry_hbond_refined 0.138 r_metal_ion_refined 0.112 r_nbtor_other 0.089 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3899 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction