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Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 NANODROP, 14.0% PEG 4000, 24.227% 2-propanol, 5.0% Glycerol, 0.1M Citric acid pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.532 α = 90 b = 61.211 β = 90 c = 113.699 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 mirror (vertical focusing) 2008-02-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97910 SSRL BL11-1
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 1.5 29.553 100 0.083 0.083 6.4 3.9 56237 15.783
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 1.5 1.54 100 0.707 0.707 1.1 3.9 4115
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 MAD THROUGHOUT 1.5 29.553 56166 2816 99.98 0.16 0.158 0.1659 0.189 0.1924 RANDOM 13.008
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 0.09 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 19.667 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 5.943 r_scangle_it 5.273 r_scbond_it 4.227 r_mcangle_it 2.624 r_mcbond_it 2.112 r_angle_refined_deg 1.655 r_angle_other_deg 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.228 r_dihedral_angle_4_deg 19.667 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 5.943 r_scangle_it 5.273 r_scbond_it 4.227 r_mcangle_it 2.624 r_mcbond_it 2.112 r_angle_refined_deg 1.655 r_angle_other_deg 0.974 r_mcbond_other 0.521 r_symmetry_vdw_refined 0.266 r_symmetry_vdw_other 0.226 r_nbd_refined 0.211 r_nbd_other 0.195 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.095 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2148 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction