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Crystal structure of human monoacylglycerol lipase in complex with compound 4f
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M NaOAc pH 5.5, 32-38% MPD
Crystal Properties Matthews coefficient Solvent content 3.26 62.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.894 α = 90 b = 127.168 β = 73.673 c = 119.675 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 100 PIXEL DECTRIS EIGER X 16M 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 49.06 98.9 0.123 0.143 0.072 0.994 4.1 3.9 79270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.35 97.9 0.728 0.854 0.439 0.868 3.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ZUN 2.3 48.191 78322 3834 97.734 0.241 0.2392 0.2508 0.2689 0.2802 82.049
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] -2.257 -2.694 -8.109 7.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.528 r_dihedral_angle_4_deg 15.903 r_dihedral_angle_3_deg 15.327 r_lrange_it 8.99 r_dihedral_angle_1_deg 5.96 r_scangle_it 4.708 r_mcangle_it 4.275 r_scbond_it 2.918 r_mcbond_it 2.564 r_angle_refined_deg 1.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.528 r_dihedral_angle_4_deg 15.903 r_dihedral_angle_3_deg 15.327 r_lrange_it 8.99 r_dihedral_angle_1_deg 5.96 r_scangle_it 4.708 r_mcangle_it 4.275 r_scbond_it 2.918 r_mcbond_it 2.564 r_angle_refined_deg 1.127 r_nbtor_refined 0.303 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.129 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.088 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8864 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling PHASER phasing