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Crystal structure of GMP reductase from mycobacterium smegmatis.
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, HANGING DROP 291 0.03 M Magnesium chloride
0.03 M Calcium chloride
20% (v/v) Ethylene glycol
10.0% (v/v) PEG 8000
0.1 M Tris/BICINE, pH 8.5 2 VAPOR DIFFUSION, HANGING DROP 291 0.03 M Magnesium chloride
0.03 M Calcium chloride
20% (v/v) Ethylene glycol
10.0% (v/v) PEG 8000
0.1 M Tris/BICINE, pH 8.5 3 VAPOR DIFFUSION, HANGING DROP 291 0.03 M Magnesium chloride
0.03 M Calcium chloride
20% (v/v) Ethylene glycol
11.5% (v/v) PEG 8000
0.1 M Tris/BICINE, pH 8.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.06 α = 90 b = 109.83 β = 119.429 c = 200.82 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 S 6M 2021-05-13 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 2.8 43.73 99.89 0.1555 0.1575 0.02519 1 17.77 39.7 118145 94.66
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 2.8 2.9 99.94 3.968 4.018 0.6261 0.662 1.07 40.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1zfj 2.8 43.7268094132 1.33786841327 118059 5903 99.9212878326 0.236369725587 0.234286072604 0.2409 0.274950470775 0.2786 random selection 114.339674134
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 12.3840003748 f_angle_d 1.22104371939 f_chiral_restr 0.0539937513943 f_bond_d 0.00991484754362 f_plane_restr 0.00964722368175
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25837 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling PHASER phasing