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Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PNP and galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CZ9 PDB ENTRY 2CZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 295 2.5% PEG 4000, 50mM magnesium chloride, 0.1M MES, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.02 39.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.333 α = 90 b = 39.067 β = 109.5 c = 81.418 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 100 IMAGE PLATE RIGAKU RAXIS V mirrors 2005-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 1.7 30 98.9 0.086 12.7 3 34628 34247 -1
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) 1.7 1.74 99.3 0.364 3.2 3.1 2438
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2CZ9 1.7 15 32846 32846 1731 98.76 0.181 0.17897 0.17672 0.1768 0.22132 0.2214 RANDOM 14.432
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] -0.56 -0.3 0.14 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.326 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_1_deg 5.792 r_scangle_it 3.875 r_scbond_it 2.488 r_mcangle_it 1.451 r_angle_refined_deg 1.395 r_mcbond_it 0.953 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.326 r_dihedral_angle_4_deg 16.432 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_1_deg 5.792 r_scangle_it 3.875 r_scbond_it 2.488 r_mcangle_it 1.451 r_angle_refined_deg 1.395 r_mcbond_it 0.953 r_nbtor_refined 0.313 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.094 r_metal_ion_refined 0.017 r_bond_refined_d 0.011 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_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 2816 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement BSS data collection SCALEPACK data scaling