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Crystal structure of GMP reductase from mycobacterium smegmatis in complex with GMP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2 M Sodium chloride
20% (v/v) PEG 3000
0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.788 α = 76.916 b = 105.098 β = 81.857 c = 170.468 γ = 69.013
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 S 6M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 47.69 90.06 0.1364 0.185 0.1241 0.992 5.27 2.1 208443 48.86
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 2.589 86.46 1.632 2.22 1.495 0.293 0.58 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 1zfj 2.5 47.6888947297 1.95835944193 205620 10161 90.0692537157 0.265159235491 0.263053609633 0.2657 0.306029421929 0.3076 57.9802898605
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 13.3532799866 f_angle_d 1.08717409398 f_chiral_restr 0.0396953907414 f_bond_d 0.0228396762407 f_plane_restr 0.00350053848762
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 52676 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 384
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling PHASER phasing