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Crystal structure of a nuclear GTP-binding protein from Encephalitozoon cuniculi bound to GDP-Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QG4 PDB ENTRY 1QG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 EncuA.01002.a.A1 PS00532 at 44.6 mg/mL with 5 mM GDP against CSHT screen condition H2: 0.1 M HEPES, pH 7.5, 20% PEG10000, cryoprotectant: 20% ethylene glycol, crystal tracking ID 225457h2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.01 38.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.57 α = 90 b = 89.25 β = 108.06 c = 54.98 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 CCD RIGAKU SATURN 944+ VariMax 2012-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 96.3 0.038 34.93 9.1 36266 34910 -3 27.426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 89.1 0.308 5.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QG4 1.8 50 34887 1740 96.37 0.1772 0.1752 0.216 0.2027 RANDOM 23.4712
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] 1.16 -0.33 -0.82 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_4_deg 21.141 r_dihedral_angle_3_deg 12.01 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.395 r_angle_other_deg 0.835 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_4_deg 21.141 r_dihedral_angle_3_deg 12.01 r_dihedral_angle_1_deg 6.572 r_angle_refined_deg 1.395 r_angle_other_deg 0.835 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3021 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 59
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction