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Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FYD 3FYD, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 PEG 8000 (14-16%), 25 MM MES, 50 MM NH2SO4, 7 MM MGCL2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.528 α = 90 b = 66.276 β = 107.52 c = 62.008 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku Varimax Confocal Optics 2008-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.6 36.85 94.8 0.035 27.2 7 41383 39244 35.4
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) 1 1.6 1.66 61.6 0.293 4.6 5.15 4129
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 3FYD, chain A 1.6 22 35290 3921 94.83 0.18414 0.18094 0.1934 0.21211 0.2239 RANDOM 41.155
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] 0.08 -0.39 -0.16 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.173 r_dihedral_angle_4_deg 18.469 r_dihedral_angle_3_deg 12.2 r_scangle_it 9.81 r_scbond_it 7.727 r_dihedral_angle_1_deg 5.366 r_mcangle_it 4.739 r_mcbond_it 3.825 r_angle_refined_deg 1.139 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.173 r_dihedral_angle_4_deg 18.469 r_dihedral_angle_3_deg 12.2 r_scangle_it 9.81 r_scbond_it 7.727 r_dihedral_angle_1_deg 5.366 r_mcangle_it 4.739 r_mcbond_it 3.825 r_angle_refined_deg 1.139 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.096 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2073 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 43
Software Software Software Name Purpose CrystalClear data collection PHENIX model building REFMAC refinement d*TREK data reduction d*TREK data scaling PHENIX phasing