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Crystal structure of mannose 6-phosphate isomerase bound with zinc and yttrium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Micro-bactch under oil 6.5 293 0.1 M magnesium acetate, 0.2 M
sodium cacodylate pH 6.5, 20% PEG 8000, 5% dioxane, 10mM zinc chloride, 10mM yttrium chloride, Micro-bactch under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.98 α = 90 b = 92.36 β = 90 c = 111.49 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2008-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.94 30 96.5 0.061 0.037 18.9 4.5 27871 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2 83.3 0.29 0.15 4.2 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1PMI 1.94 28.95 1 26445 1406 97.56 0.18439 0.18174 0.1822 0.23649 0.2356 RANDOM 16.992
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] 0.03 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.621 r_dihedral_angle_4_deg 14.765 r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 5.931 r_scangle_it 3.44 r_scbond_it 2.026 r_mcangle_it 1.276 r_angle_refined_deg 1.202 r_mcbond_it 0.674 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.621 r_dihedral_angle_4_deg 14.765 r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 5.931 r_scangle_it 3.44 r_scbond_it 2.026 r_mcangle_it 1.276 r_angle_refined_deg 1.202 r_mcbond_it 0.674 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2967 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 22
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling