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X-ray structure of NikA in complex with HBED
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.26 45.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.083 α = 90 b = 93.848 β = 90 c = 124.731 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 4 2008-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.8 46.93 95 0.044 23.31 5.3 90975 33.1
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) 1.8 88 0.396 4.19 5.3 12358
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 1ZLQ 1.8 46.93 90300 4753 100 0.18432 0.1825 0.1822 0.21894 0.2189 RANDOM 26.231
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] 0.2 -0.96 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.485 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 13.556 r_dihedral_angle_1_deg 6.147 r_scangle_it 3.456 r_scbond_it 2.14 r_angle_refined_deg 1.347 r_mcangle_it 1.312 r_mcbond_it 0.706 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.485 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 13.556 r_dihedral_angle_1_deg 6.147 r_scangle_it 3.456 r_scbond_it 2.14 r_angle_refined_deg 1.347 r_mcangle_it 1.312 r_mcbond_it 0.706 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7909 Nucleic Acid Atoms Solvent Atoms 762 Heterogen Atoms 193
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling