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Crystal structures of zinc containing Adenylate kinase from Desulfovibrio gigas
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M TARTRATE NA/K, 0.1 M MES (PH 6.5) AND 20% PEG 2K OR 8K (THE PROTEIN:WELL SOLUTION RATIO IN THE DROP WAS 1:1, 1:2 OR 1:3 WITH THE FINAL DROP VOLUME OF 4, 6 OR 8 MICRO LITRE)
Crystal Properties Matthews coefficient Solvent content 3.59 65.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.39 α = 90 b = 119.44 β = 90 c = 149.59 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.8 23.19 99.5 0.07 10.2 6 31474 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) 1 1.8 1.85 95.5 0.34 1.6 6
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 MAD THROUGHOUT NONE 1.8 23.92 31474 1671 99.53 0.17967 0.17793 0.1968 0.21152 0.2264 RANDOM 14.049
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] 0.13 -0.08 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.751 r_dihedral_angle_4_deg 22.409 r_dihedral_angle_3_deg 16.215 r_scangle_it 6.289 r_dihedral_angle_1_deg 5.814 r_scbond_it 3.865 r_angle_refined_deg 2.214 r_mcangle_it 2.081 r_mcbond_it 1.276 r_chiral_restr 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.751 r_dihedral_angle_4_deg 22.409 r_dihedral_angle_3_deg 16.215 r_scangle_it 6.289 r_dihedral_angle_1_deg 5.814 r_scbond_it 3.865 r_angle_refined_deg 2.214 r_mcangle_it 2.081 r_mcbond_it 1.276 r_chiral_restr 0.207 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1718 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling autoSHARP phasing