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Crystal structure of glycerol kinase from Cellulomonas sp. NT3060
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 277 27-37% MPD, 0.1M citrate, pH 4.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.43 α = 90 b = 105.43 β = 90 c = 195.715 γ = 90
Symmetry Space Group P 41 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 MARRESEARCH 2003-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.130 SPring-8 BL41XU
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 2.3 55.9 99.2 0.104 5.8 9.1 50338 49935
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.42 99.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SIROAS THROUGHOUT 2.3 20 49643 49643 2521 99.9 0.19535 0.19535 0.19293 0.1959 0.24046 0.242 RANDOM 30.327
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] 0.1 0.1 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.584 r_scangle_it 4.204 r_dihedral_angle_1_deg 3.824 r_scbond_it 2.619 r_angle_refined_deg 1.593 r_mcangle_it 1.581 r_mcbond_it 0.859 r_symmetry_vdw_refined 0.384 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.584 r_scangle_it 4.204 r_dihedral_angle_1_deg 3.824 r_scbond_it 2.619 r_angle_refined_deg 1.593 r_mcangle_it 1.581 r_mcbond_it 0.859 r_symmetry_vdw_refined 0.384 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.236 r_chiral_restr 0.189 r_xyhbond_nbd_refined 0.168 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 7754 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SOLVE phasing