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Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with Tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 30% MPD, 100mM Tris-HCl, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.01 α = 90 b = 92.01 β = 90 c = 267.235 γ = 120
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 210 2012-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.67 50 99.2 0.059 37 5.5 96185
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 1.67 1.73 98.2 0.318 6.5 5
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 2Z07 1.67 32 91313 4825 98.96 0.14695 0.14558 0.159 0.17272 0.1839 RANDOM 18.197
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 33.748 r_dihedral_angle_4_deg 14.281 r_dihedral_angle_3_deg 11.977 r_dihedral_angle_1_deg 5.386 r_angle_other_deg 3.49 r_angle_refined_deg 1.314 r_chiral_restr 0.08 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.748 r_dihedral_angle_4_deg 14.281 r_dihedral_angle_3_deg 11.977 r_dihedral_angle_1_deg 5.386 r_angle_other_deg 3.49 r_angle_refined_deg 1.314 r_chiral_restr 0.08 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 6839 Nucleic Acid Atoms Solvent Atoms 674 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling MOLREP phasing Coot model building