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Crystal structure of a non-biological ATP binding protein with a TYR-PHE mutation within the ligand binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G4B PDB ENTRY 3G4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M SODIUM PHOSPHATE PH 8.5, 0.25 M SODIUM CITRATE, 0.3 M SODIUM CHLORIDE, 23% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 4.21 70.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.107 α = 90 b = 71.107 β = 90 c = 55.935 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 4 2008-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B NSLS X12B
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 2.7 50 99.3 0.135 15.385 4.2 4710
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) 2.7 2.8 99.4 0.57 4.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3G4B 2.7 41.42 4702 216 99.8 0.204 0.202 0.2015 0.238 0.2358 RANDOM 32.69
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 r_dihedral_angle_2_deg 31.296 r_dihedral_angle_3_deg 14.941 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_1_deg 5.586 r_scangle_it 3.127 r_scbond_it 1.844 r_angle_refined_deg 1.691 r_mcangle_it 1.253 r_mcbond_it 0.629 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.296 r_dihedral_angle_3_deg 14.941 r_dihedral_angle_4_deg 12.411 r_dihedral_angle_1_deg 5.586 r_scangle_it 3.127 r_scbond_it 1.844 r_angle_refined_deg 1.691 r_mcangle_it 1.253 r_mcbond_it 0.629 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 582 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 54
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling