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Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose
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 5.5 293 30% MPD, 100 mM sodium citrate buffer, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.445 α = 90 b = 93.445 β = 90 c = 254.141 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 270 2011-11-19 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 1.77 50 99.3 0.045 51.3 5.6 80188
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 1.77 1.83 100 0.208 10.8 4.8
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 1.77 29.74 76054 4028 99.25 0.15985 0.15841 0.1721 0.18692 0.2003 RANDOM 25.11
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 33.533 r_dihedral_angle_4_deg 16.135 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 5.677 r_long_range_B_refined 5.33 r_long_range_B_other 5.199 r_scangle_other 3.539 r_angle_other_deg 3.502 r_mcangle_it 2.267 r_mcangle_other 2.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.533 r_dihedral_angle_4_deg 16.135 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 5.677 r_long_range_B_refined 5.33 r_long_range_B_other 5.199 r_scangle_other 3.539 r_angle_other_deg 3.502 r_mcangle_it 2.267 r_mcangle_other 2.267 r_scbond_it 2.196 r_scbond_other 2.196 r_mcbond_it 1.5 r_mcbond_other 1.499 r_angle_refined_deg 1.422 r_chiral_restr 0.091 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 6691 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling MOLREP phasing Coot model building