☰ Navigation Tabs
Acylphosphatase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2 M AS 30% w/v PEG4K
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.415 α = 90 b = 81.944 β = 90 c = 63.994 γ = 90
Symmetry Space Group C 2 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 PIXEL DECTRIS EIGER X 4M 2021-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.55 41.97 99 0.094 0.109 0.053 0.998 10.2 6.5 3631 68.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.67 0.981 0.44 1.5
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 (All) 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 2.552 41.006 3630 162 98.534 0.208 0.2049 0.2142 0.2782 0.291 RANDOM 67.18
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] -1.259 2.055 -0.796
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.205 r_lrange_other 15.196 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_6_deg 12.575 r_scangle_it 11.988 r_scangle_other 11.71 r_mcangle_other 8.544 r_mcangle_it 8.538 r_dihedral_angle_2_deg 8.118 r_scbond_it 7.78
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.205 r_lrange_other 15.196 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_6_deg 12.575 r_scangle_it 11.988 r_scangle_other 11.71 r_mcangle_other 8.544 r_mcangle_it 8.538 r_dihedral_angle_2_deg 8.118 r_scbond_it 7.78 r_scbond_other 7.593 r_dihedral_angle_1_deg 7.316 r_mcbond_it 6.033 r_mcbond_other 5.988 r_angle_refined_deg 1.675 r_angle_other_deg 0.548 r_symmetry_xyhbond_nbd_refined 0.366 r_symmetry_nbd_other 0.195 r_nbd_refined 0.193 r_nbtor_refined 0.171 r_nbd_other 0.161 r_symmetry_nbd_refined 0.148 r_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_xyhbond_nbd_other 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 732 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHENIX phasing