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Crystal structure of enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1M Calcium acetate hydrate, 0.1M MES PH=6.0, 15% v/vPEG 400
Crystal Properties Matthews coefficient Solvent content 2.38 48.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.343 α = 90 b = 78.803 β = 123.68 c = 167.11 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 PIXEL DECTRIS PILATUS3 6M 2024-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.987 SSRF BL18U1
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 2.5 50 99.8 0.209 0.227 0.087 0.937 2.8 6.8 75645
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 2.5 2.54 99.6 0.664 0.718 0.271 0.797 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.51 48.94 1.34 70361 1983 92.22 0.2069 0.2049 0.2062 0.2738 0.2737
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.205 f_angle_d 1.053 f_chiral_restr 0.052 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14916 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling