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Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of (the JCSG+ condition #G8) 0.15M DL-Malic acid, 19% PEG 3350 and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci).
Crystal Properties Matthews coefficient Solvent content 2.37 48.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.479 α = 90 b = 128.12 β = 90 c = 209.646 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 225 mm CCD Beryllium Lenses 2014-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 40 97.7 0.135 0.14 0.055 4.8 7.3 98973
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 95.2 0.472 0.747 6.9 4779
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4OLQ 2.1 40 93373 4923 97.65 0.2 0.1984 0.2074 0.2321 0.2363 RANDOM 33.663
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] -1.19 1.29 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_3_deg 14.683 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_1_deg 5.653 r_mcangle_it 2.128 r_angle_other_deg 1.576 r_angle_refined_deg 1.489 r_mcbond_it 1.29 r_mcbond_other 1.29 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_3_deg 14.683 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_1_deg 5.653 r_mcangle_it 2.128 r_angle_other_deg 1.576 r_angle_refined_deg 1.489 r_mcbond_it 1.29 r_mcbond_other 1.29 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_bond_other_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11687 Nucleic Acid Atoms Solvent Atoms 1153 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data collection MOLREP phasing HKL-3000 data reduction