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Crystal structure of adenylate kinase from Marinibacillus marinus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S3G PDB ID 1S3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 283 0.5 % LDAO,150 mM sodium chloride 1.5 M tri-Sodium citrate, 9mM p1,p5-Di(adenosine-5')pentaphosphate pentasodium salt, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.639 α = 90 b = 46.506 β = 98.67 c = 62.669 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 IMAGE PLATE RIGAKU RAXIS IV Rigaku Osmic Mirrors 2008-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54
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 2 33.42 98.7 0.029 24 2.81 18017 17786 3
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) 2 2.07 96.9 0.08 9.4 2.46
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 PDB ID 1S3G 2 20 17786 16895 901 98.86 0.18275 0.18043 0.1842 0.22606 0.1805 RANDOM 19.117
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] 0.32 -0.34 -0.5 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.374 r_dihedral_angle_3_deg 18.026 r_dihedral_angle_4_deg 11.364 r_dihedral_angle_1_deg 5.721 r_scangle_it 5.007 r_scbond_it 3.04 r_angle_refined_deg 1.931 r_mcangle_it 1.737 r_mcbond_it 0.885 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.374 r_dihedral_angle_3_deg 18.026 r_dihedral_angle_4_deg 11.364 r_dihedral_angle_1_deg 5.721 r_scangle_it 5.007 r_scbond_it 3.04 r_angle_refined_deg 1.931 r_mcangle_it 1.737 r_mcbond_it 0.885 r_chiral_restr 0.133 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 1674 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 58
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling