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Crystal structure of a stable adenylate kinase variant AKlse2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 1.9M ammonium citrate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.293 α = 90 b = 47.202 β = 90 c = 109.328 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 100 CCD ADSC QUANTUM 270 2013-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9795 PAL/PLS 7A (6B, 6C1)
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 1.8 50 99.9 19437 19418
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4MKG 1.8 50 18446 18376 992 99.62 0.17382 0.17125 0.1807 0.22247 0.2295 RANDOM 25.634
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] -0.95 -0.07 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.278 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_4_deg 12.165 r_long_range_B_refined 7.403 r_long_range_B_other 7.354 r_dihedral_angle_1_deg 5.748 r_scangle_other 5 r_scbond_it 3.168 r_scbond_other 3.167 r_angle_other_deg 2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.278 r_dihedral_angle_3_deg 12.949 r_dihedral_angle_4_deg 12.165 r_long_range_B_refined 7.403 r_long_range_B_other 7.354 r_dihedral_angle_1_deg 5.748 r_scangle_other 5 r_scbond_it 3.168 r_scbond_other 3.167 r_angle_other_deg 2.551 r_mcangle_other 2.473 r_mcangle_it 2.469 r_angle_refined_deg 2.331 r_mcbond_it 1.745 r_mcbond_other 1.705 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1674 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 58
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling