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Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PN 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 38.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.945 α = 90 b = 38.997 β = 109.6 c = 81.188 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 2005-07-16 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 1.45 30 98.5 0.077 14.4 3 53991 -1.5
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 1.45 1.48 96.6 0.478 2.3 2.7
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2CZ9 1.5 20 47224 2535 98.7 0.189 0.187 0.1862 0.228 0.2251 RANDOM 15.95
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] -0.43 -0.47 0.26 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.838 r_dihedral_angle_4_deg 14.614 r_dihedral_angle_3_deg 12.103 r_dihedral_angle_1_deg 5.985 r_scangle_it 3.344 r_scbond_it 2.209 r_mcangle_it 1.366 r_angle_refined_deg 1.294 r_mcbond_it 0.867 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.838 r_dihedral_angle_4_deg 14.614 r_dihedral_angle_3_deg 12.103 r_dihedral_angle_1_deg 5.985 r_scangle_it 3.344 r_scbond_it 2.209 r_mcangle_it 1.366 r_angle_refined_deg 1.294 r_mcbond_it 0.867 r_nbtor_refined 0.309 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.085 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_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 2749 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement BSS data collection SCALEPACK data scaling