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Crystal structure of psychrotrophic esterase EstA from Pseudoalteromonas sp. 643A inhibited by monoethylphosphonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IVN PDB entry 1IVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein solution: 15 mg/ml Protein, 20 mM HEPES pH 7.5, 250 mM NaCl, 5 % Glycerol. Well solution: 1.6 M Na/K phosphate, 100 mM HEPES pH 7.5. Both solutions mixed 1:1 in drops, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.19 61.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.82 α = 90 b = 83.82 β = 90 c = 130.95 γ = 120
Symmetry Space Group P 61 2 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 CCD MARMOSAIC 300 mm CCD mirrors 2008-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.35 30 100 0.069 38.751 14 60202
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 1.35 1.4 100 0.68 11.8
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 PDB entry 1IVN 1.35 30 60116 3052 99.93 0.1731 0.17228 0.1974 0.18867 0.2111 RANDOM 11.984
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] -0.11 -0.06 -0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.559 r_dihedral_angle_4_deg 27.165 r_dihedral_angle_3_deg 12.513 r_dihedral_angle_1_deg 4.853 r_scangle_it 4.551 r_scbond_it 3.035 r_mcangle_it 1.87 r_angle_refined_deg 1.856 r_mcbond_it 1.093 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.559 r_dihedral_angle_4_deg 27.165 r_dihedral_angle_3_deg 12.513 r_dihedral_angle_1_deg 4.853 r_scangle_it 4.551 r_scbond_it 3.035 r_mcangle_it 1.87 r_angle_refined_deg 1.856 r_mcbond_it 1.093 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1440 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction MOLREP phasing