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Crystal structure of Gpb in complex with 4a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.8 289 10mM BES buffer
Crystal Properties Matthews coefficient Solvent content 2.57 52.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.46 α = 90 b = 128.46 β = 90 c = 116.58 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD MAR CCD 165 mm 2014-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0403 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 38.36 99.7 0.078 11.6 4.6 90140 6609
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99.9 4.2 4.5
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 4MHO 1.8 38.36 85720 4420 99.67 0.17546 0.1743 0.1752 0.19762 0.1988 RANDOM 29.946
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] 0.76 0.76 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.183 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 14.482 r_dihedral_angle_1_deg 5.572 r_long_range_B_refined 5.521 r_mcangle_it 2.186 r_scbond_it 2.075 r_mcbond_it 1.34 r_angle_refined_deg 1.291 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.183 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 14.482 r_dihedral_angle_1_deg 5.572 r_long_range_B_refined 5.521 r_mcangle_it 2.186 r_scbond_it 2.075 r_mcbond_it 1.34 r_angle_refined_deg 1.291 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6556 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement SCALA data scaling DENZO data reduction MOSFLM data reduction