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MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH GDP-Mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BO7 PDB ENTRY 2BO7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 4% V/V ETHYLENE GLYCOL, 0.1 M BIS-TRIS PROPANE, PH 5.5, 0.3 M MAGNESIUM FORMATE
Crystal Properties Matthews coefficient Solvent content 5.58 78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.5 α = 90 b = 149.5 β = 90 c = 154.321 γ = 120
Symmetry Space Group P 32 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 120 IMAGE PLATE MAR scanner 345 mm plate OSMIC VARIMAX HF MIRRORS 2009-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.7 23.4 96.8 0.12 9.5 5.4 47729 2 47.09
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 2.7 2.85 98.8 0.55 2.8 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BO7 2.7 129.47 47729 2704 96.12 0.19279 0.19136 0.21878 0.199 RANDOM 40.369
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] -0.09 -0.05 -0.09 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 19.49 r_dihedral_angle_3_deg 18.646 r_dihedral_angle_1_deg 5.953 r_scangle_it 3.791 r_scbond_it 2.233 r_angle_refined_deg 1.601 r_mcangle_it 1.519 r_mcbond_it 0.767 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 19.49 r_dihedral_angle_3_deg 18.646 r_dihedral_angle_1_deg 5.953 r_scangle_it 3.791 r_scbond_it 2.233 r_angle_refined_deg 1.601 r_mcangle_it 1.519 r_mcbond_it 0.767 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other 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 6189 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing