☰ Navigation Tabs
Crystal Structure of D,D-heptose1.7-bisphosphate phosphatase from E. coli in complex with calcium and phosphate
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, 0.005M sodium phosphate, 11% glycerol
, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.79 31.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.183 α = 90 b = 50.446 β = 90 c = 52.018 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 2008-09-05 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 1.95 39.65 88.5 0.055 13.5 3.79 11271 11271 1 1 31.76
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 1.95 2.02 98.2 0.34 3.2 3.33 1245
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 1.95 39.65 1 1 10728 10728 540 87.9 0.21149 0.20843 0.2108 0.27598 RANDOM 34.351
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] -0.89 -0.18 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.937 r_dihedral_angle_3_deg 16.1 r_dihedral_angle_4_deg 15.706 r_dihedral_angle_1_deg 14.649 r_scangle_it 4.135 r_scbond_it 2.812 r_angle_refined_deg 1.791 r_mcangle_it 1.559 r_mcbond_it 1.025 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.937 r_dihedral_angle_3_deg 16.1 r_dihedral_angle_4_deg 15.706 r_dihedral_angle_1_deg 14.649 r_scangle_it 4.135 r_scbond_it 2.812 r_angle_refined_deg 1.791 r_mcangle_it 1.559 r_mcbond_it 1.025 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.272 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.227 r_metal_ion_refined 0.215 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.118 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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 108 Heterogen Atoms 7
Software Software Software Name Purpose CrystalClear data collection PHENIX model building REFMAC refinement CrystalClear data reduction CrystalClear data scaling PHENIX phasing