☰ Navigation Tabs
Crystal structure of haloacid dehalogenase-like hydrolase family enzyme from Staphylococcus lugdunensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M sodium formate, 0.2M ammonium acetate, 0.2M sodium citrate tribasic dihydrate, 0.2M sodium potassium tartrate tetrahydrate, 0.2M sodium oxamate, 10% w/v PEG 4000, 20% v/v glycerol, 0.1M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.947 α = 90 b = 121.387 β = 90 c = 134.405 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 PIXEL DECTRIS PILATUS3 6M 2022-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.73 58.86 98.6 0.997 9.3 1.8 62991
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 0.895
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.73 58.86 59847 3141 98.21 0.15328 0.15086 0.19931 0.2034 RANDOM 22.82
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] 2.84 0.37 -3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.704 r_dihedral_angle_2_deg 9.136 r_dihedral_angle_1_deg 6.199 r_long_range_B_refined 5.684 r_rigid_bond_restr 5.524 r_long_range_B_other 4.662 r_scangle_other 2.647 r_mcangle_other 2.352 r_mcangle_it 2.35 r_scbond_it 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.704 r_dihedral_angle_2_deg 9.136 r_dihedral_angle_1_deg 6.199 r_long_range_B_refined 5.684 r_rigid_bond_restr 5.524 r_long_range_B_other 4.662 r_scangle_other 2.647 r_mcangle_other 2.352 r_mcangle_it 2.35 r_scbond_it 1.779 r_scbond_other 1.778 r_angle_refined_deg 1.581 r_mcbond_it 1.576 r_mcbond_other 1.575 r_angle_other_deg 0.554 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3648 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing