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Crystal structure of glycerol kinase in complex with glycerol from Sinorhizobium meliloti 1021
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2M Na-malonate, pH 7.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.22 α = 90 b = 101.975 β = 90.03 c = 107.548 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M Mirrors 2011-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9790 NSLS X25
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 2.32 50 99.3 0.06 7.9 7.2 86871 86871
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 2.32 2.4 93.4 0.58 2 5.5
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 (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 2.33 47.57 86871 81631 4303 99.86 0.23311 0.23011 0.2288 0.28993 0.2857 RANDOM 49.038
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] -0.02 0.02 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.607 r_dihedral_angle_4_deg 22.575 r_dihedral_angle_3_deg 20.666 r_dihedral_angle_1_deg 7.097 r_scangle_it 3.828 r_scbond_it 2.651 r_angle_refined_deg 1.671 r_mcangle_it 1.526 r_mcbond_it 0.833 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.607 r_dihedral_angle_4_deg 22.575 r_dihedral_angle_3_deg 20.666 r_dihedral_angle_1_deg 7.097 r_scangle_it 3.828 r_scbond_it 2.651 r_angle_refined_deg 1.671 r_mcangle_it 1.526 r_mcbond_it 0.833 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14215 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 21
Software Software Software Name Purpose CBASS data collection AutoSol phasing PHENIX model building Coot model building CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing CCP4 phasing