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The structure of wt A. thaliana IGPD2 in complex with Mn2+ and phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 290 0.1 M Bicine, pH 9.0, 10% w/v PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.65 53.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.13 α = 90 b = 225.13 β = 90 c = 225.13 γ = 90
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 315 2008-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9507 Diamond I02
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 1.75 71.19 99.4 0.118 11.7 4.2 187811 187811
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 1.75 1.84 99.4 0.579 2.2 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 45.98 178465 9330 99.34 0.13154 0.12901 0.1398 0.17949 0.1902 RANDOM 20.568
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_sphericity_bonded 36.666 r_dihedral_angle_2_deg 32.591 r_sphericity_free 21.545 r_rigid_bond_restr 16.299 r_dihedral_angle_4_deg 13.239 r_dihedral_angle_3_deg 12.256 r_scbond_it 9.266 r_scbond_other 9.028 r_scangle_other 7.693 r_dihedral_angle_1_deg 6.38
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 36.666 r_dihedral_angle_2_deg 32.591 r_sphericity_free 21.545 r_rigid_bond_restr 16.299 r_dihedral_angle_4_deg 13.239 r_dihedral_angle_3_deg 12.256 r_scbond_it 9.266 r_scbond_other 9.028 r_scangle_other 7.693 r_dihedral_angle_1_deg 6.38 r_long_range_B_refined 6.251 r_long_range_B_other 6.251 r_mcangle_it 3.483 r_mcbond_it 3.346 r_mcbond_other 3.338 r_mcangle_other 3.196 r_angle_refined_deg 1.532 r_angle_other_deg 1.171 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11506 Nucleic Acid Atoms Solvent Atoms 1304 Heterogen Atoms 80
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling