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Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with Tris and D-glycerate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.4M potassium sodium tartrate, 0.1M HEPES-NaOH (pH 7.5), 50mM calcium chloride, 10mM D-glycerate
Crystal Properties Matthews coefficient Solvent content 2.43 49.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.94 α = 90 b = 92.94 β = 90 c = 190.401 γ = 120
Symmetry Space Group P 3 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 CCD ADSC QUANTUM 270 2013-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 2.1 50 97.6 0.11 9.3 4.6 55067
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 2.1 2.21 93.6 0.19 5.5 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.1 45.145 52252 2809 97.52 0.24653 0.24472 0.2561 0.27971 0.2683 RANDOM 30.159
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.787 r_dihedral_angle_4_deg 15.827 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 5.671 r_long_range_B_refined 4.909 r_long_range_B_other 4.883 r_angle_other_deg 3.556 r_scangle_other 2.731 r_mcangle_it 2.515 r_mcangle_other 2.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.787 r_dihedral_angle_4_deg 15.827 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 5.671 r_long_range_B_refined 4.909 r_long_range_B_other 4.883 r_angle_other_deg 3.556 r_scangle_other 2.731 r_mcangle_it 2.515 r_mcangle_other 2.515 r_scbond_it 1.678 r_scbond_other 1.677 r_mcbond_it 1.609 r_mcbond_other 1.609 r_angle_refined_deg 1.394 r_chiral_restr 0.128 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6796 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data processing SCALA data scaling MOLREP phasing Coot model building SCALEPACK data reduction