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Crystal structure of adenylate kinase from Methanococcus maripaludis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KHT PDB ENTRY 1KHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.7 273 3.4 M ammonium chloride, 0.1 M sodium acetate, 3% ethylene glycol (v/v)., pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.84 α = 90 b = 102.84 β = 90 c = 228.72 γ = 120
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 2008-08-28 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 2.5 29.69 99.9 0.082 9.6 2.44 31194 31158 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) 2.5 2.59 100 0.33 2.3 2.4 3109
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 ENTRY 1KHT 2.5 19.7 31158 27970 3138 99.86 0.18821 0.18268 0.1815 0.23911 0.2059 RANDOM 59.467
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] 9.05 9.05 -18.1
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 32.944 f_dihedral_angle_4_deg 20.369 f_dihedral_angle_3_deg 20.275 f_dihedral_angle_1_deg 7.119 f_scangle_it 4.547 f_scbond_it 3.002 f_angle_refined_deg 2.151 f_mcangle_it 1.995 f_mcbond_it 1.12 f_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 32.944 f_dihedral_angle_4_deg 20.369 f_dihedral_angle_3_deg 20.275 f_dihedral_angle_1_deg 7.119 f_scangle_it 4.547 f_scbond_it 3.002 f_angle_refined_deg 2.151 f_mcangle_it 1.995 f_mcbond_it 1.12 f_chiral_restr 0.124 f_bond_refined_d 0.022 f_gen_planes_refined 0.009 f_bond_other_d f_angle_other_deg f_gen_planes_other f_nbd_refined f_nbd_other f_nbtor_refined f_nbtor_other f_xyhbond_nbd_refined f_xyhbond_nbd_other f_metal_ion_refined f_metal_ion_other f_symmetry_vdw_refined f_symmetry_vdw_other f_symmetry_hbond_refined f_symmetry_hbond_other f_symmetry_metal_ion_refined f_symmetry_metal_ion_other f_mcbond_other f_rigid_bond_restr f_sphericity_free f_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5848 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 228
Software Software Software Name Purpose CrystalClear data collection PHASER phasing PHENIX refinement REFMAC refinement d*TREK data reduction d*TREK data scaling