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Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 apoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVL PDB ENTRY 2WVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2
Crystal Properties Matthews coefficient Solvent content 3.6 65.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.456 α = 90 b = 113.456 β = 90 c = 195.982 γ = 90
Symmetry Space Group P 41 21 2
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.97 45.2 99.4 0.11 19.5 18.9 26864
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 2.97 3.1 96.7 1.27 2.2 18.5
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 PDB ENTRY 2WVL 2.97 42.91 25502 1358 99.57 0.20122 0.19779 0.1932 0.26636 0.2583 RANDOM 71.327
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] -0.17 -0.17 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.463 r_dihedral_angle_3_deg 22.474 r_dihedral_angle_4_deg 20.301 r_dihedral_angle_1_deg 6.693 r_angle_refined_deg 1.731 r_scbond_it 1.175 r_scangle_it 1.09 r_mcangle_it 0.38 r_mcbond_it 0.209 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.463 r_dihedral_angle_3_deg 22.474 r_dihedral_angle_4_deg 20.301 r_dihedral_angle_1_deg 6.693 r_angle_refined_deg 1.731 r_scbond_it 1.175 r_scangle_it 1.09 r_mcangle_it 0.38 r_mcbond_it 0.209 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 6076 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing