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Crystal Structure of the Y103F mutant of the GDP-mannose mannosyl hydrolase in complex with GDP-mannose and MG+2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 5mM GDP-mannose
5mM glucose
5mM GDP-mannose
5mM glucose
100 mM Tris HCL p8.5
20% PEG 4000, 0.2 Mg Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.87 68.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.785 α = 90 b = 93.893 β = 91.23 c = 66.103 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 315 2004-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 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 2.3 50 97.6 0.072 14.3 3 36595
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) 2.3 2.38 99.9 0.406 3 3717
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RYA 2.3 77.61 111382 36594 1883 97.55 0.188 0.188 0.186 0.226 RANDOM 40.589
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] 0.99 -0.49 -3.06 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.544 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 5.917 r_scangle_it 2.469 r_scbond_it 1.655 r_angle_refined_deg 1.223 r_mcangle_it 1.172 r_mcbond_it 0.688 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.544 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_3_deg 15.345 r_dihedral_angle_1_deg 5.917 r_scangle_it 2.469 r_scbond_it 1.655 r_angle_refined_deg 1.223 r_mcangle_it 1.172 r_mcbond_it 0.688 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.198 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3906 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 142
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MADNESS data reduction AMoRE phasing