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Structure of esterase Est22 with p-nitrophenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M MES, pH 5.5, 0.2M Ca(Ac)2, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.823 α = 90 b = 57.22 β = 97.46 c = 54.578 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315 2015-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 50 96.2 16.8 6.8 72570
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 5HC4 1.4 50 62736 3321 90.58 0.13292 0.13157 0.1313 0.15808 0.158 RANDOM 16.075
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 0.22 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.248 r_dihedral_angle_4_deg 15.329 r_dihedral_angle_3_deg 11.488 r_long_range_B_refined 8.446 r_long_range_B_other 8.445 r_dihedral_angle_1_deg 6.319 r_scangle_other 4.525 r_scbond_it 3.088 r_scbond_other 3.073 r_angle_refined_deg 2.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.248 r_dihedral_angle_4_deg 15.329 r_dihedral_angle_3_deg 11.488 r_long_range_B_refined 8.446 r_long_range_B_other 8.445 r_dihedral_angle_1_deg 6.319 r_scangle_other 4.525 r_scbond_it 3.088 r_scbond_other 3.073 r_angle_refined_deg 2.393 r_mcangle_it 2.145 r_mcangle_other 2.145 r_mcbond_it 1.589 r_mcbond_other 1.568 r_angle_other_deg 1.214 r_chiral_restr 0.152 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing