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Crystal structure of human esterase D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PV1 PDB ENTRY 1PV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 289 200mm ammonium acetate, 30% PEG4000, pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.78 30.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.542 α = 90 b = 70.724 β = 108.84 c = 65.014 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 CCD ADSC QUANTUM 315 mirrors 2008-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 50 98.1 0.325 0.325 20.5 3.6 70703 69289 2 2 15.5
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) 1.5 99.6 0.325 0.325 20.5 3.6 69289
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PV1 1.5 40.16 2 2 69289 65767 3500 100 0.1786 0.17685 0.17581 0.1786 0.19612 0.1957 RANDOM 17.953
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] -0.58 -0.26 0.73 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.342 r_dihedral_angle_4_deg 12.432 r_dihedral_angle_3_deg 11.193 r_dihedral_angle_1_deg 5.489 r_scangle_it 2.93 r_scbond_it 2.417 r_sphericity_bonded 2.36 r_rigid_bond_restr 2.325 r_sphericity_free 1.431 r_mcangle_it 1.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.342 r_dihedral_angle_4_deg 12.432 r_dihedral_angle_3_deg 11.193 r_dihedral_angle_1_deg 5.489 r_scangle_it 2.93 r_scbond_it 2.417 r_sphericity_bonded 2.36 r_rigid_bond_restr 2.325 r_sphericity_free 1.431 r_mcangle_it 1.253 r_angle_refined_deg 1.032 r_mcbond_it 0.655 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4293 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling