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Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.95 293 sodium acetate, PEG 400, DTT, 2-methyl-2, 4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.76 α = 90 b = 54.28 β = 92.2 c = 70.15 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 PILATUS 6M-F 2014-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972957 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.35 46.97 98.1 0.036 0.999 18.37 4.36 75872 -3 25.092
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 1.35 1.38 95.7 0.56 2.31 4.23
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 4Q0H 1.35 39.37 72086 3795 98.07 0.1422 0.1407 0.1405 0.1709 0.171 RANDOM 25.474
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] 0.08 -0.2 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.039 r_sphericity_free 30.668 r_sphericity_bonded 13.888 r_dihedral_angle_4_deg 12.91 r_dihedral_angle_3_deg 11.684 r_dihedral_angle_1_deg 6.327 r_mcangle_it 2.235 r_scbond_it 2.134 r_mcbond_it 1.675 r_rigid_bond_restr 1.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.039 r_sphericity_free 30.668 r_sphericity_bonded 13.888 r_dihedral_angle_4_deg 12.91 r_dihedral_angle_3_deg 11.684 r_dihedral_angle_1_deg 6.327 r_mcangle_it 2.235 r_scbond_it 2.134 r_mcbond_it 1.675 r_rigid_bond_restr 1.654 r_angle_refined_deg 1.506 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2335 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 63
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction