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Crystal structure of B. globisporus adenylate kinase variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 2.5M ammonium sulfate, 1% polyethylene glycol 1000, 0.1% Sodium azide, 50mM HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.106 α = 90 b = 65.106 β = 90 c = 94.565 γ = 120
Symmetry Space Group P 31 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 100 CCD ADSC QUANTUM 210r 2011-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 2.1 50 99.8 53.98 21.6 13990
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 2.1 2.18 100 0.508 21.9
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 1S3G 2.1 50 13143 683 98.79 0.19679 0.1931 0.2022 0.27611 0.2844 RANDOM 49.319
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] -0.16 -0.08 -0.16 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.414 r_dihedral_angle_4_deg 16.465 r_dihedral_angle_3_deg 15.244 r_long_range_B_other 7.313 r_long_range_B_refined 7.312 r_dihedral_angle_1_deg 6.077 r_scangle_other 5.698 r_mcangle_it 4.299 r_mcangle_other 4.299 r_scbond_it 3.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.414 r_dihedral_angle_4_deg 16.465 r_dihedral_angle_3_deg 15.244 r_long_range_B_other 7.313 r_long_range_B_refined 7.312 r_dihedral_angle_1_deg 6.077 r_scangle_other 5.698 r_mcangle_it 4.299 r_mcangle_other 4.299 r_scbond_it 3.84 r_scbond_other 3.838 r_mcbond_it 3.244 r_mcbond_other 3.235 r_angle_refined_deg 2.043 r_angle_other_deg 0.881 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1648 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing