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Crystal Structure of Calcium-bound D,D-heptose 1.7-bisphosphate phosphatase from E. Coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GMW PDB Entry 2gmw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 25% PEG 3350, 0.1M Tris, 0.005M DTT, 0.025M sodium chloride, 0.005M calcium chloride, 11% glycerol
, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.81 32.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.904 α = 90 b = 50.585 β = 90 c = 52.638 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2008-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 1.7 40.62 94.2 0.047 13.9 3.64 18244 1 1 26.075
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 1.7 1.76 80 0.313 3.2 2.36 1894
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 2gmw 1.7 40.62 1 1 17299 17299 944 94.15 0.2032 0.20045 0.2009 0.25844 RANDOM 29.588
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] -1.22 -0.58 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.501 r_dihedral_angle_4_deg 20.815 r_dihedral_angle_3_deg 12.846 r_dihedral_angle_1_deg 6.729 r_scangle_it 3.622 r_scbond_it 2.502 r_angle_refined_deg 1.504 r_mcangle_it 1.376 r_mcbond_it 0.885 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.501 r_dihedral_angle_4_deg 20.815 r_dihedral_angle_3_deg 12.846 r_dihedral_angle_1_deg 6.729 r_scangle_it 3.622 r_scbond_it 2.502 r_angle_refined_deg 1.504 r_mcangle_it 1.376 r_mcbond_it 0.885 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.248 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.197 r_metal_ion_refined 0.133 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 1423 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHENIX model building REFMAC refinement CrystalClear data reduction CrystalClear data scaling PHENIX phasing