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Enterococcus casseliflavus glycerol kinase mutant HIS232ALA complexed with glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XUP PDB ENTRY 1XUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 29% PEG400, 0.1M sodium acetate, 0.1M calcium acetate, 10% glycerol, PH4.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.572 α = 90 b = 200.019 β = 90 c = 56.431 γ = 90
Symmetry Space Group P 21 21 2
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 4 2005-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
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 2.03 50 89 0.091 11.8 63332 2
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 2.03 2.1 0.261
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 PDB ENTRY 1XUP 2.03 39.28 63284 3224 88.92 0.19075 0.19075 0.194 0.249 0.201 RANDOM 26.812
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 -0.25 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.692 r_dihedral_angle_4_deg 21.927 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_1_deg 8.576 r_scangle_it 5.96 r_scbond_it 4.313 r_mcangle_it 2.639 r_angle_refined_deg 2.594 r_mcbond_it 1.979 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.692 r_dihedral_angle_4_deg 21.927 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_1_deg 8.576 r_scangle_it 5.96 r_scbond_it 4.313 r_mcangle_it 2.639 r_angle_refined_deg 2.594 r_mcbond_it 1.979 r_nbtor_refined 0.317 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.222 r_symmetry_hbond_refined 0.217 r_chiral_restr 0.213 r_xyhbond_nbd_refined 0.17 r_bond_refined_d 0.038 r_gen_planes_refined 0.015 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 7676 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 12
Software Software Software Name Purpose XFIT data reduction REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling