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Crystal structure of SdgB (complexed with phosphate ions)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 1.2 M NaH2PO4, 0.8 M K2HPO4, and 0.1 M CAPS-NaOH (pH 10.5)
Crystal Properties Matthews coefficient Solvent content 3.82 67.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.257 α = 90 b = 172.257 β = 90 c = 106.174 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 287 CCD ADSC QUANTUM 270 2014-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.2 50 89 0.973 16.9 8.2 26949
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 0.916
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 7EC1 3.2 29.98 25550 1357 88.84 0.1993 0.1961 0.2099 0.2597 0.2623 RANDOM 60.717
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] -0.1 -0.05 -0.1 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.148 r_dihedral_angle_4_deg 20.18 r_dihedral_angle_3_deg 18.186 r_dihedral_angle_1_deg 7.744 r_angle_refined_deg 1.376 r_angle_other_deg 1.113 r_chiral_restr 0.056 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.148 r_dihedral_angle_4_deg 20.18 r_dihedral_angle_3_deg 18.186 r_dihedral_angle_1_deg 7.744 r_angle_refined_deg 1.376 r_angle_other_deg 1.113 r_chiral_restr 0.056 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8254 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing