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X-ray structure of the reduced NikA/1 hybrid, NikA/1-Red
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZLQ PDB ENTRY 1ZLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 293 1.8M ammonium sulfate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.967 α = 90 b = 94.616 β = 90 c = 125.025 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 CCD ADSC QUANTUM 315r Mirrors 2008-11-28 M 0.9796
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 47.3 97 0.056 22.63 7 110957 25.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 93 0.315 5.9 6.6 16443
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 1ZLQ 1.7 47.3 107953 5682 100 0.16601 0.16401 0.1741 0.20374 0.2098 RANDOM 18.032
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] -0.01 0.11 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.407 r_dihedral_angle_4_deg 16.129 r_dihedral_angle_3_deg 13.929 r_dihedral_angle_1_deg 6.565 r_scangle_it 5.7 r_scbond_it 3.583 r_mcangle_it 2.331 r_angle_refined_deg 2.256 r_mcbond_it 1.445 r_chiral_restr 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.407 r_dihedral_angle_4_deg 16.129 r_dihedral_angle_3_deg 13.929 r_dihedral_angle_1_deg 6.565 r_scangle_it 5.7 r_scbond_it 3.583 r_mcangle_it 2.331 r_angle_refined_deg 2.256 r_mcbond_it 1.445 r_chiral_restr 0.223 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7892 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 137
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling