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Crystal structure of possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 277 15.0% Ethanol, 0.2M MgCl2, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.624 α = 90 b = 119.462 β = 90 c = 151.274 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2006-06-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97932, 0.91837, 0.97915 SSRL BL9-2
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 2.1 29.323 100 0.152 0.152 4.4 3.7 70192 20.6
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) 2.1 2.15 100 0.635 0.635 1.2 3.7 5087
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 (All) 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 MAD THROUGHOUT 2.1 29.323 70121 3531 99.92 0.181 0.18146 0.179 0.1887 0.234 0.2462 RANDOM 23.291
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] -0.59 0.53 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.842 r_dihedral_angle_4_deg 15.681 r_dihedral_angle_3_deg 13.952 r_scangle_it 7.049 r_dihedral_angle_1_deg 6.433 r_scbond_it 5.194 r_mcangle_it 2.842 r_mcbond_it 1.837 r_angle_refined_deg 1.433 r_angle_other_deg 0.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.842 r_dihedral_angle_4_deg 15.681 r_dihedral_angle_3_deg 13.952 r_scangle_it 7.049 r_dihedral_angle_1_deg 6.433 r_scbond_it 5.194 r_mcangle_it 2.842 r_mcbond_it 1.837 r_angle_refined_deg 1.433 r_angle_other_deg 0.972 r_mcbond_other 0.383 r_symmetry_vdw_other 0.246 r_nbd_refined 0.209 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.161 r_nbtor_other 0.086 r_chiral_restr 0.082 r_metal_ion_refined 0.029 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8884 Nucleic Acid Atoms Solvent Atoms 1035 Heterogen Atoms 138
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing